Stacking cooldowns is generally one of the worse things you can do unless if damage spikes occur very erratically or not often.
I would normally agree with you, but I don't think you understand how weak Tree of Life and Nature's Vigil are as healing cooldowns by themselves.
I haven't played my Shaman since Cata, so I took some time to look up the class again. It looks like your raid cooldowns are:
Healing Tide - Strong AoE heal (like Tranquility)
Spirit Link - Localized damage-resistance + health redistribution
Ascendance - Basically +100% healing for AoE situations
I think that may be the disconnect here. If you think of ToL (+15% healing) and NV (+20%/+10% healing) as equivalent to your Ascendance (+100% healing), then yes, it would be a horrible waste to pop both those cooldowns together.
(which is also why spirit shell is great on its 1 minute cooldown, but thats another topic)
You cite Spirit Shell as a good example of a short healing cooldown. Indeed, it looks like it would be nice to have a few pre-casted Prayer of Healings before a timed spike.
I'm trying to think how that would apply to a 5.2 Nature's Vigil, and I just don't see it. I suppose I could pop it 10s before a spike and Rejuv up each member of the raid, but that would eat up over 20% of my mana pool. Also, Rejuv only lasts 12s, so that's a lot of wasted ticks.
Maybe that's a hint at the real issue. Druids lack spammable burst AoE heals like Prayer of Healing, so we need bursty cooldowns to make a meaningful impact during spikes. Smoothing out our cooldowns is much more harmful than the math would indicate.
I am not misunderstanding at all, I know how these cooldowns work. I have an active paladin and the only thing they have are multiple throughput cds (GoAK, DF, AW, and HA if you spec it). Their raidwide reduction cooldown doesn't even work on close to 1/3-1/2 the fights this tier and they don't have a tranq or anything like that (though not saying they are weak or anything, just pointing it out)
One of the worst things you can do is pop more than one of those at once for one burst (assuming it occurs fast). While none of these three are exactly super strong, ask any paladin here and you will see they also don't just use both DF and AW for, say, one RoB on wind lord, I guarantee it. And ToL is more than just a 15% boost so calling it just a 15% boost is a misnomer.
You forget that with my spec I have 3 more cooldowns that I have access to that a normal shaman does not. EM, + 2 PE elementals. And yes, I plan ahead for every burst so that I will have ONE of these 6 cooldowns for said encounters at specific bursts (either a PE, an EM, a HTT, or ascendance). SLT is also sometimes added in there, but half the time isn't because it is not possible to position it always on more than half the fights this tier.
Edit - additionally on the 7-8 fights that I use it, SLT is one of those cooldowns I plan with my raid ahead of time since I don't always get to use that at free will. The other 5 though, are under my control.
Right now one of the biggest resto shaman buffs we are getting is EM on a 1 minute cooldown. Even if they halve the duration or cut the haste in half, it becomes much much stronger than it used to be and more people will spec it. Same idea is being applied here.
As an aside, here is what my heroic blade lord cooldown rotation is like - it only works since I have access to a crapton of cooldowns. With regards to shaman, I am not saying nature's swiftness is bad (its our competition for the tier - the best portion is the instant cast portion, not the passive haste), but by spec'ing right you will have a cooldown up each time.
hit 1) ascendance + SLT (raid wanted) + PE
2) SWG + EM + PE
4) ascendance + SLT + maybe an SWG
5) maybe an swg + EM
You will only get 5 if your dps is good enough so that means HTT, ascendance and even EM will eventually be back in phase 2.
Only reason I added this last part is that I am explaining how forethought to cooldowns can be very strong on some fights.
Also about the burst thing, GC said they are revamping shrooms since they suck for the role they are supposed to fill (which i assumed was aoe burst, but they really suck). having that also fixed will go a long way.