The Gym issue was an issue in G/S/C too. I wish they'd have fixed it.. They did buff Falkner's Pokemon in this one, and the first few gyms seem to be appropriately leveled and such, but after that it just falls off.
I didn't overtrain or grind my Pokemon so they'd stay at about the same level or slightly lower than gym ones (and I only carry 4) and I found it to be much more fun, but I feel like I shouldn't have to "go easy" on a game.
This older thread I made a while ago (don't revive it or anything) had some ideas on how to make it harder and more fun, like playing with only one Pokemon type, etc.