Mostly agreed, but the ability to nova could easily be limited by having some abilities such as spell slots replenish only partially on a short rest, much like the wizard's Arcane Recovery feature. It could even stipulate the same "only spell slots of 5th and lower can be recovered" limitation or whatever else makes sense.
If being guaranteed at least one spell (or smite or whatever) per encounter is unacceptable, then maybe implement some kind of diminishing returns, i.e. each short rest recovers fewers resources than the previous until they no longer regain anything at all except perhaps hit points (by spending HD).
I don't think converting everything to short rest mechanics is necessary, but it could certainly be made to work without crippling the current encounter design.