I would argue that cooldown management would then be the new resource management. Managing cooldowns is a lot easier since you will time your abilities to what the boss is doing. But, more on that later since someone else also touched upon this. I also think it is a lot easier for the developers to balance cooldowns against balancing focus and focus gain.
I have played wow a lot, mostly as a Brewmaster, Prot Warrior and Guardian Druid in wod/legion. And the ‘‘resources’’ there are a lot more balanced. And as you level you can use your abilities more easily since you achieve a net neutral state. The most comparable thing to the current focus system would be, I think, Guardian Druid. Since you would have to prep rage to deal with boss mechanics. I think in that setting the tradeoff makes sense. Since you have a balanced ‘‘resource’’ system, cooldowns and a lot more abilities.
If focus is here to stay. Then the end goal should be to create a net neutral state. Where it doesn’t matter what you do, you will always have enough focus. To me that is too limiting since you will only reach that as you reach the end of the game. And from an outsider perspective it seems like a balancing nightmare with, focus potions, affixes. I do think rune cooldowns are required, regardless with what they decide.
It’s a pretty controversial take yeah, haha.
I disagree that channeling/animation time and cooldowns are comparable, since they are too different in what they do. Animation/channeling time is more relevant to punishment windows. Whereas, cooldowns are a resource similar to how focus is a resource. But, the limiting factor is no longer the amount of focus but an amount of time.
I also don’t think it would slow combat down. I feel like the current focus system is what is slowing combat down for me. Not always having focus and it being a shared resource limits my options. Unless , I achieve a net neutral state, and then it becomes spam, which is unhealthy. That paired with runes dealing a lot of damage that they override the combat loop to an extent. If I can delete an enemy with 1 rune it is no longer combat, level difference also probably plays a factor.
I also disagree with the standard button routine from MMORPGs. That is mostly true for DPS players in a PVE setting; Tank and Healers only to an extent as their role is more reactive. But, I think it is better to compare it to PVP in MMORPGs. Where you save certain abilities for certain enemy abilities.
You can also compare it to V Rising where you use dashes, attacks, counters, ranged attacks, weapon skills and shields in a reactive manner to the boss. And managing cooldowns becomes the resource management.
I think it is a worthwhile tradeoff 
It makes balancing for the devs easier, we get more varied combat quicker. And cooldowns become the new resource management. Which, honestly, I prefer over focus management. Since it is easier to predict. You internalize when a certain ability has an 8 second cooldown. It is much harder to think about how many hits equals enough focus for Rune 2.
I don’t know what focus would be then. Maybe investing into it increases rune damage?
I do think it is contingent on runes having a specific purpose like:
- AOE
- Buffs
- Dodge
- Parry
- Ultimate
- Reflect
- Leap
I do like the combo suggestion of chaining runes together, would be so sick. CDR reduction could become available as an affix or something.
Also would you be so kind to further specify what you mean with the following. I feel like I am missing something 