1: Skill affixes are limited to a number of skills.
2: Skill affixes are limited to "enhancing" a particular skill in only one way (like crit %, lower CD, lower resource cost, etc...).
Essentially only a few skills affixes are actually useful. Critical hit chance is probably the best followed by damage, reduced cost, and then cool downs (of course this is subject to a player's build).
My possible solution: Allow all skills to be available on skill affixes (not passives) and have multiple benefits available for the skills so that players can have access to more viable builds. Also simplify the affix on items so that it will be more like + Random Demon Hunter Skill Bonus rather then list all of the skills and different rolls which wastes room and space on the item. Also perhaps allow rare rings/amulets to roll skill affixes.
Example: Say my Demon Hunter finds an item that has + Random Demon Hunter Skill Bonus and it rolls Rain of Vengeance.
Initially the bonus for Rain of Vengeance could be something like *Lowers Cool Down by X and increases damage by Y*
Now if you find another item with the same Rain of Vengeance affix perhaps another bonus could be applied that is more visual. Something like *For X seconds chilling Ice Arrows will fall from the sky with Y% chance to freeze once you use this skill dealing Z% damage*. So even though you might use a rune that lasts for 5 seconds this additional bonus might even continue for a longer duration.
Also to make build diversity/customization even more favorable, skill affixes on items would produce TWO affixes rather then one. So my Demon Hunter could have the Rain of Vengeance AND a Sentry bonus to my skills.
This way seeing a skill affix come up on an item won't be a chance of disappointment, but could allow the player to see the opportunity in changing their build and seeing an improvement from that.
TLDR: -Allow all skills to roll on skill affixes (not passives).
-Allow each skill affix to add more then one bonus (so for meteor you could get Less Arcane Cost + More % Damage.
-Also if you have another skill affix that you already have it would add an additional effect to that skill (for meteor the impact would make the meteor also burst into fragments that deal X% amount of damage each).
-Rolling a skill affix would instead give you two different skill affix bonuses (for the same class) rather then just one, increasing build diversity even further and making skill affixes more useful.
-Perhaps allow rare rings and amulets the ability to also roll skill affixes.