You do realize that situations like this work because the only real 'choice' you have in these scenarios is your gear, right? And that the things you mention have minimum iLvl restrictions to make sure that you're not thrown into a dungeon you really couldn't handle? And that dungeons in those instances are generally tuned to work with any of the classes...?
As far as being called out only applying to 'top-tier-high-end-game-world-first-parties'... I've gotten called out and kicked from Fractal for not pulling the whole damned first room because the healer was undergeared and I was worried about heals, so don't go telling me it's not something that doesn't happen outside of World First Prog.
2 reasons: First, a bad rotation is easy to spot and usually can be something that is address -in progress-. A bad build can be as much as choosing one skill wrong and can either be quick to fix or require a lenghtly conversation and isn't something that can be altered within a dungeon.
Second: It creates artificial complexity and introduces a wild card where-in if, say, I am playing with a WHM I will always know which skills they will have at a specific level. At 60 you will always have the same skillset regardless of the rest of gear or anything else. In a build-based system there's always the possibility of 'opting out' of a skill like Benediction, or for a PLD 'opting out' of Flash.
Imagine this conversation, the first is with guaranteed skills:
"Why don't you use Flash?"
"Because I don't like using it."
Second, with possible choice:
"Why don't you use Flash?"
"Because I chose <skill x> over it."
With option 1 you can explain why a tank can be using Flash and reason them into it. With option 2... you get into DF with that and you're stuck either kicking them, leaving or dealing with no AoE emnity control. Yes, I know that with careful planning on the Dev side this wouldn't be an issue, but it's something they would have to spend an inordinate amount of time on to make sure the content they have isn't broken when the skill system comes out..... or spend time rebalancing the old content to work with the new system.