They're definitely not fine lol. The way you are referring to them being utilized IE blowing up auto pilot set play stuff is fine! I don't want that to change, nor would it be if recovery time was added, because the true balanced purpose of PP should be just that: shutting down predictable stuff.
The problem is that it's way too powerful a technique for how random, non-committal, and inexpensive it is, to the point where it doesn't just shut down predictable stuff. It also "aw shucks, look what happened here, lol"'s you into advantageous/disadvantageous situations out of nowhere.
If I knock you down with Marisa and drive rush into st fierce and you perfect parry because I'm predictable, that's perfectly fine, but let's say 1 million dollars at Capcom Cup is on the line and you just happen to perfect parry my normal; not because you scouted an autopilot set play on my behalf and shut it down, but because you just happened to press the button unintentionally at the perfect time to PP my standing medium kick, a traditional safe/non-commital poke for the majority of the roster, and had the meter to convert that that into SA3 and win the game.
A pro player is never going to find the above scenario acceptable because it takes away from the skill and adds a random, oftentimes unintentional scenario to the mix.
Gotta keep in mind that many of the things lower level/casual players find to be fun and dope is because it was designed with them in mind and not the actual experts/masters of the craft. Me and
@Hiei ran some sets earlier, and while we're both pretty good players, we're nowhere near pro level, yet still I can think of scenarios where one of just happened to "Aw shucks, guess what I did LOL" perfect parry ourselves into a win.
Punk has said from the jump that PP is busted and hates it, many of the best players echo his sentiments. This scenario below is a perfect example of how insanely powerful and game shifting it can be.
I don't think "JUST BE LESS SOLID AND DO RANDOM STUFF" is a good solution to this lol.