That might be a problem (-_-'). That is because I've been working on MIDIs from Pokemon DPPt and BW for a "project" (I can't say much on that lol). PM if you want to try some MIDIs :).
No, they will not sound the same, though I wish they did ^^' The instruments sound a bit "duller" in the game then they do if you just played the song in a MIDI player...