Some people basically have to be limited by system design. Giving them a choice is not effective for them. I think a hybrid system could work.
This is why you find some people in CO who're subscribed but playing archetypes anyway. Because they don't want to deal with the hassle of a freeform build, or tried it and what they came up with didn't work so they went back to something they know does. And I agree, that kind of premade build should be provided for anyone to use in a freeform game. Perhaps not as absolute as CO's archetypes are and certainly not mechanically inferior like they are (Freeform players get two more powers total than an archetype does), but they definitely need to be there. Personally I would simply build a more traditional 'powerset' in the freeform system and then offer that to players as an option if they want to just get straight to beating up bad guys.
As for a hybrid system where using one power sets a cooldown on another, STO has something like that. (In itself, STO uses another pretty close to freeform system) The way they do it is having abilities grouped into categories based on what system they use. So using Attack Pattern Alpha sets off a short cooldown on all other Attack Pattern abilities, using Emergency Power to Shields sets off a cooldown on all other Emergency Power abilities, etc. Given that some abilities in any given category can do wildly different things it sets up an interesting metagame of what to use when. Or it would, but Cryptic. I think the idea is sound though, especially for really powerful abilities to ensure you can't have your Elude or Unstoppable or whatever active and also start blowing people up with Inferno or Nova at the same time.
You know, this is very interesting and while not directly on topic is on subject with power sets because sometimes the type of powers can be or how they can be implemented sometimes depend on the system design.
True, CoH often had a lot of powers that were essentially the same thing at different power levels especially in attack sets, and other powers that could easily have been combined into one, all those toggles in every defensive set. But at the same time, having nine slots to fill out gave them the opportunity to make things like support and control sets have a lot of variety. While in CO the lower number of powers means those sorts of things are inherently going to be simplified. An attack or defense set doesn't lose much if you condense your three single target blasts into one chargeable power and your four defensive toggles into one slotted passive, but control and especially support lose a lot because a single power that does what three support powers together would do in CoH is considered overpowered in the eyes of most people.
Personally, I'm more than willing to accept a little redundancy when it comes to simpler concepts if it means the more complicated ideas are allowed to exist without having to lose anything.
You know, maybe we should take this to a new thread.