Every Nintendo console since the Gamecube has had one and every handheld since the GBA except the 3DS has had two so it's almost even, actually. The original was on both the GBA and GCN, then came Twisted for the GBA, then came Touched for the DS, then Smooth Moves for the Wii, then DIY for the DS, and then Game and Wario for the Wii U last year.
Regarding the ATs and Pokemon, I figured this was going to be the case from the get-go. Aside from the roster (which I'm still mildly suspicious about), they're putting a lot of emphasis on both versions having different content so I can see them having different AT/Pokemon and they will probably have completely different unlockable ATs. I also imagine that the two can be transferred between each other once both games are out.