Hi. WD has been my main forever, and I'm just going to go over most of the skills and give some ideas and comments. Took your format, also agree on a lot of your suggestions, so we may have some overlap.
Primaries: I think they all should be free also, though the mana cost I guess is negligable most of the time. I think having primaries synergize with certain skills would really boost their usage, because at the moment most people just forgo them.
Poison Dart - Increase damage across all runes.
Splinters: It's fine but possibly add in something like enemies in its close proximity can also get hurt by the splinters(sort of like a small aoe dmg aura around the monster). I sort of imagine these splinters sticking out of the monster and hurting those around it also. Not stackable(but you can cast on other monsters, will require you to micro)
Numbing Dart: Increase slow to where it's actually useful. Maybe like beyond just slowing enemy movement, it would slow by 20% every second for 5 seconds until it comes to a full stop before being able to move again. Could also consider slowing enemy attack speed too(would open possibility to new builds - tanking, etc)
Spined Dart: I feel like this would be nice as a dot.
a) 5 seconds you could be gaining x amount of mana each second(so you could cast on multiple guys for big mana boost)
B) enemies pierced with spined dart lose control of their mana and resources - releasing energy into the air... As long as you are in an aoe around the enemy you gain x% increased resource regen(would also work for your party)
Flaming Dart: Increase damage, or give another effect like:
a) enemy gains movement speed but loses accuracy while on fire
B) fire can spread to other monsters
c) monster damage taken is increased by x% while on fire.
Snake to the Face: Buff the chance to stun. Also give some more effects while the snake is stuck on the enemy.
Corpse Spiders: Buff damage
Spider Queen: I think this skill needs a full rework.
a) While spider queen is out, it has a chance to lay eggs in enemies it attacks. When the enemy dies, spiders will explode out of the enemy causing AOE dmg, or maybe just extra leaping spiders.
B) Walks around and lays Spider Sac mines. Enemies that step on the spider sacs get dealt X% of dmg, and are slowed/webbed for 1 second.
c) Allow us to have more than 1 out at a time.
Medusa Spiders - more slow, or possible webbing, other crazy poison effects(blind, confusion, bleed)
Blazing Spiders: More Damage. Leaves an immolation trail, enemies walk over it take x% dmg.
Plague of Toads - remove mana cost. I think all runes except rain of toads and toad of hugeness have a lot of trouble hitting monsters due to the random pathing. I think the random pathing is fine but a few changes would go a long way to making this an useful skill.
a) Toads stay around until they hit something
B) Toads dont explode on obstacles, they will jump around obstacles.
c) Toads jump around in a circle around you.
d) Toads can pierce.
If you can make it actually work to hit monsters and everything then I think the runes are okay(well except for toad of hugeness and toad affinity)
Toad of Hugeness: This skill is just useless in its current incarnation. Few ideas here
a) Make it a constant pet with some sort of aura that helps you. Maybe it can grow with each monster it eats, and after a max of 5 monsters it will give some buff, or give you access to a bonus attack(such as toad of hugeness has eaten too much and explodes for x% dmg in an aoe)
B) Allow multiple casts, and allow it to be able to eat elites.
c) Boost mana regen while eating enemies
d) Taunts enemies.
Toad Affinity: Spawn more frogs?
Firebomb : Increase damage. This is the primary I'm most okay with, but overall it can still use a bit of tweaks.
Pyrogeist needs to be stackable.. other runes just need a bit of damage adjustment.
Would love a rune that gives a vortex effect.
Grasp of the dead: Overall I think this is a pretty good skill. The slow becomes less valuable at higher difficulties... Maybe adjust the mana cost a little bit?
For Death is life: Maybe give it a little higher % chance, also if you have max dogs, I would love for the spell to be able to spawn additional temporary dogs, on top of the ones you have already.
Rain of corpses: Doesn't really seem like a rain, the damage is pretty pathetic also.
Desperate Grasp: 2 seconds doesnt mean very much... remove cooldown fully, allow stacks, or give it something else.
Dire bats - This skill needs a lot of help. Since the skill change in 1.08, you can't really move around and use dire bats anymore. Maybe lower the mana cost A LOT. or make this the only one that isnt a channeling rune.
Vampire Bats - maybe a bit more life steal, and also allow the bats to stay for a few seconds after you stop casting, so you can cast vampire bats for some sustain before moving on to different skills.
Plague bats and cloud of bats are pretty good now. Though I think cloud of bats needs just a TINY TINY bit of radius increase, at least to where melee guys get hit by it. Sometimes your channeling and monsters are hitting you, but you arent hitting them...
Hungry Bats - Possibly increase proc rate, or damage? Or give them a little haunt effect. Since they are hungry, they may attack one target then go after another one for 2 hits.
Haunt - Damage isn't great. Allow stacking up to a certain amount.
Consuming Spirit - 155 hp a second is basically negligable. Should probably be a %.
Resentful Spirit - more damage or bit more duration
Lingering Spirit - Pretty decent if stacking is allowed, for more stacking.
Grasping Spirit - 30% slow is essentially useless. Allow stacking of slow, or possible etherealness. For example Grasping Spirit pulls enemy into the spirit world, causing them to take additional damage from spells, and doing less physical damage.
Draining Spirit- Maybe a % based mana regen, or allow stacking.
Locust Swarm: I think all the runes should have the pestilence effect. Possibly allow stacking also, damage is rather useless at high difficulty levels.
If that change happens... then Pestilence will need to be adjusted.
Cloud of insects is pretty terrible: The duration isn't needed and at the low damage its not helpful. Would love if this was maybe more like Maghda's projectile. A slow moving cloud of insects, infecting anything in its path. Also causes blind.
Devouring Swarm -regen X mana per second.
Diseased Swarm: very few monsters are actually going to be killed by locust swarm... maybe just change it to monsters that die while under the effect of diseased swarm leave a pool of poison. Or enemies affected by diseased swarm take extra poison damage.
Searing Locusts: More damage.
Zombie Dogs - Buff damage. Allow Circle of life to spawn additional temporary dogs(last for 30 seconds) on top of your currently summoned dogs. If not buffing damage, give the different runes some aoe buff effects. Such as resource regeneration, life regeneration, bonus dps, life steal, etc.
Allow procing again?
Horrify: The concept is just a bit problematic, if you fear things, it just makes it harder to kill them. Maybe make it a reverse taunt kind of spell, where enemies do run away but not to the point where you lose sight of them and they don't come back. It's not fun chasing enemies all over the map.
Phobia: Enemies take increased damage? It'd make fearing the enemies actually somewhat worthwhile.
Face of death: Maybe it creates a bubble that enemies are scared to enter, but outside the bubble they will still congregate. This gives you a bit of safety net without having the monsters run all over the map.
Other runes are okay.
Spirit Walk is a great skill, but mandatory for every WD essentially. Doesn't really need a change. All the runes are pretty useful, although I would love if umbral shock gave you a firechains with your decoy body, rather than exploded.
Hedge Magic: Make this a % based spell.
Angry Chicken: Increase damage. Allow you to lay egg mines, which explode for some damage.
Painful Transformation - The damage is pretty useless... Increase it, or it could maybe transform the monster and give you a clone(like d2 revive but less strong)
Unstable Form: Slight buff to AOE.
Soul Harvest - good spell.
Languish - maybe more slow or duration.
Sacrifice: Mostly pretty good. Maybe allow us to sacrifice fetishes and gargantuans also? Gargantuans would do more damage, fetishes would do a bit less since you can have more.
Black Blood: I like Firezombies idea about increasing your and allies movespeed.
Provoke the pack: Good, but it really needs a good buff icon rather than just the aura under your feet.
Devolution: Not just confused enemies have chance to spawn. Also if you already have max dogs, the extra dogs spawned become temporary dogs- so you could have like 4 regular dogs and 3 temporary dogs.
Unstable Realm - Not that useful...
Mass Hallucination: More damage. Or maybe allow monsters to attack the phantom(draws monster attacks away from you)
Zombie Charger: Essentially all the runes besides bears needs a lot of work.
Leperous Zombie - Increase distance, increase duration of poison, increase damage?
Undeath: Instead of on death make it on hit,would love to see a cascading chain of zombies spawning due to it. Limit of 2 times.. could be increased.
Wave of Zombies: MOAR ZOMBIES. Would also love it if they were very slow moving, but formed a powerful wall that knocked enemies back, or carried them back with them.
Explosive Beast: More damage, or more beasts, or more radius. And maybe an aoe dot effect, after the beast explodes, it immolates the ground and enemies within the area take X% dmg over x seconds.
Spirit Barrage: I love this spell, but all of them feel sort of weak. I believe all of the spells should come with the well of souls rune effect built in. It's supposed to be a Barrage! One little laserish thing isn't a barrage...
Spirit is willing - Maybe make it work like rush of essense - x mana return over x seconds.
Well of Souls - more damage or even more spirits shooting out. 3 spirits isn't exactly a well.
Phantasm - Increase Duration or damage, or aoe.
Phlebotomize - More Regen/life leech. Possibly could allow everyone to leech from the phlebotomized enemy. Gives a debuff that lasts for a few seconds.
Manitou - More damage, or more casts, higher proc rate.
Acid Cloud: Make it stackable!
Kiss of Death and Corpse Bomb need some adjustments... Would love it if corpse bomb was more like corpse explosion from necromancer in d2, maybe those that are under its dot effect also explode for a bit of damage.
Zombie Wall: I really like this spell but it just isn't that great. lower the cooldown. Why can't we have multiple walls out? Add this into tribal rites too?
Creepers: Buff damage and # of Creepers.
Pileon - Reduce Cooldown.
Dead Rush - Reduce Cooldown
Gargantuan: I love the spell just wish it still had proc rates. Maybe give the different runes some different aura effects.
Wrathful protector: Still lasts a short time, but gives you/party increased 15% attack speed/dmg also. Or it could constantly taunt enemies also.
Maybe all the runes could give a tiny bit of aoe aura effect - reduce enemy damage, life link, etc. GG
Or they could grow more powerful with kills.
Big Bad Voodoo: Pretty good skill all around.
Boogie Man: Allow you to spawn additional dogs if you already have max dogs. Current dogs also get some sort of boost while Boogie Man is active. And can also give a boost to other pets such as fetishes also.
Fetish Army: I agree with fire zombie that fetishes from our passive need to not disappear when this skill is cast. Overall needs a buff in damage, possibly a little buff to survivability. I have a lot of memories of fetishes from D2(My godly HC barb was murdered by a combination of lag and extra strong, cursed, phys immune extra fast, exploding and i forget what else fetish), and though they were brittle their damage was really nothing to laugh at. They do nothing right now.
Fetish Ambush: Not really an ambush, 250% damage is really low also. Buff damage or allow it to have some other effects... such as lowering enemy resists/defenses by 25% for X amount of time. It'd fit because the enemies were ambushed and thus caught by surprise.
Pierce the Veil: Lower the Mana increase... Or increase the damage... Or make it so its not applicable on all skills. I think its worth it if it works for our damage skills, but if we have it on and just casting primaries/grasp of the dead means we run out of mana.... then its not great.
Bad Medicine: Also increases your poison damage by a little bit. Would allow for some real poison based builds. Or lowers enemies poison resistance.
Fetish Syncopants: Adjust the ratios for different skills. overall buff the % chance... Allow spawning of tiki torchers, headhunters, different types of fetishes. Maybe occasionally an ultra rare fetish general which gives aoe boost to speed.
Zombie Handler: Increase pet damage also? Maybe expand it to include fetishes also...
Rush of Essence: Offer some more buffs besides just the mana return. Maybe soul harvest can have 1 or 2 more stacks with rush of essence... or it allows you to stack more spirit spells.
Fierce Loyalty: This needs a change... just not sure what.
Tribal Rites: Add more skills into this passive... like wall of zombies.
Circle of Life: Allow you to spawn additional temporary dogs if you already have the max amount of dogs summoned.
These are my basic thoughts.