Team Aqua and Magma literally got almost no fire type or water type pokemons, they feel like you are battling agaisnt team rocket with all these Zubat, Koffing, Grimer and Medhyena. They could of at least gave Fire, Ground and Rock types for Magma and Water and Ice type for Aqua. When you keep getting the same Dark and Poison type it's kind of boring, mostly when they are not that hard to begin with.
They do at least use the Numel and Carvanha lines, but they're not seen as often as the constant spam of the Zubat and Poochyena lines. That's the main problem I see with villain teams, is the presence of too many Dark and Poison-types.
As for my thoughts on the games, from what I've seen I have mixed reactions, They did make some stuff easier (like Feebas no longer being restricted to certain tiles) but they also have some annoying things as well, like the Strength puzzles reverting back to pre-5th Gen mechanics and Route 113's ash collecting now being a more frustrating process.
But again, I do have to credit Game Freak for retaining a lot of the nostalgia while still making it fresh at the same time. It's one of those things that is very hard to balance.