The danger to this is that the expectation will be a perfect lineup. Fighting Latios or Latias? You don't have 6 perfect maxed level Rayquazas? Then you're doing it wrong.
The game remains interesting because people have to find different solutions to the problems presented. Want to solo Machamp? Mewtwo is good. Don't have that, try Espeon, or Double Flying Rayquaza, or Lugia, or Ho-Oh. We all have choices, with different costs, different strengths and weaknesses (Lugia crushes fighting Machamp, but isn't great vs. double Steel Machamp, etc.)
So there would have to be curbs and limits on things. Finding a pokemon with 15 attack, 15 defense, and 6 stamina shouldn't set one off on a quest to jack that stamina up 9 points. But it's doable, and it would be nice to be able to buff up 98% or 96% pokemon to 100%. Just not too much, and it should cost a lot.