And by "3D Pokemon games" do you mean the ones on the 3DS or the ones on, say the GameCube or earlier? Because those games were sequenced. You'll just have a rougher time working with the GameCube ones because it uses Nintendo's proprietary format. It's been converted to midi, just not perfectly. (No reverb, pitch bending, or GM standards.)
And as for the 3DS games, those are all sequenced.