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Late on the Miltank discussion, but I do admit when I first played HG I had problems with that gym, but nowadays I usually have a decent counter for it so the battle is easier.
It is? I've seen Omastar on occasions with Shell Smash, but I can't recall ever facing a Kabutops, not that I play a lot competitively though. I've always been a fan of dinosaurs and other ancient animals, so I really love all the fossil Pokémon.
I can't really point to a single favorite, but I really liked all of Unova's Gyms, they all had their completely unique style and lovely remixes of the standard Gym Musics. In comparison to these, the previous generations' Gyms look very bland and boring.