I think they should drop the label of "prestige class" or "paragon path" or "kit" or any prior term--as if it has the baggage it does in fact have--and then build something new that meets the design goals. Preferably, this should be done either as part of or after the design of a functional multi-class system, since no doubt it will at least nudge that part of the design. Then if when this is working, they need a good name for it, and one of those labels fits, well so be it.
If they want to talk about elements that a DM can use as rewards, then they are talking about something mostly outside the normal class/level structure. Let's not let that thing, whatever it is, be constrained with "(type) class" labels, surely!
As for the DM/Player control, I think that issue is a side effect of the prior lousy design of trying to shoehorn such elements into the class structure to begin with. Make the elements solid enough, and they'll work as things that a DM can use as rewards in one group, and as things that players can pick as a character crafting option in another group.