You are aware that what I said also means that orchestration is only "sometimes" better suited for a track than MIDI, correct?
Yes, and in the case of the two examples I proposed [Aion and Guilty Gear], they just happen to have better sound that fits my personal preferences. Though again, that doesn't discredit Pokemon X/Y's score at all.
I'm pretty sure there's never any MIDI guitar in X&Y (read: I know there isn't). The only MIDI used is for the parts of tracks that are better suited with it, just like in the Galaxy games and Skyward Sword, all three of which have ridiculously awesome music. I don't think you realize that both orchestration and MIDI have their own unique benefits, i.e. strengths over the other.
Mario Galaxy 1/2 and Skyward Sword are all right as their music goes, but X/Y has great music, especially for a Pokemon game. Anyhow, regarding the Midi guitar, just compare
this track [which happens to use heavy Midi] to the one I linked before and you'll find that their sounds are similar.
Also, I'd just like to point out that Metroid Prime still has one of the most riveting soundtracks ever composed to this day, and as far as I know, it's pure MIDI. Just sayin'.
Just so happens that I've previously listened to half of the Metroid: Other M soundtrack to try to get more into the series.... And if I recall from somewhere, it also uses Midi and pure instruments. Most of it is ambient, though, which doesn't personally suit my tastes, but the fast-paced tracks are engaging. Metroid Prime's ost consists of the the same--an otherworldly ambience because Samus is in deep space and quicker-tempo battle tracks. The only difference is that it's all in Midi, but Prime does sound better overall.