Disclaimer: although I have both an SC88Pro and an MT-32 connected and therefore know what I'm talking about, quality is a subjective term. I find it's a game-by-game case. If a game has custom sounds and was developed specifically for an MT-32, it'll likely sound better on the MT-32. The SC88 does not support those custom sounds, even in CM64 mode, and has different sounding instruments (not bad by a long shot -- probably better in many cases as the samples have been recorded at higher quality, but different, which may not be what the composer intended).
Many more recent games were developed with General MIDI in mind and only remapped to (more or less) match the samples available on the MT-32. Since the MT-32 doesn't listen to all MIDI channels by default, this can even mean some voices are dropped entirely... at least, on a real MT-32... the SC88 in emulation mode does seem to listen to those channels and actually sound better (but in that case, since the music was intended for GM, which not just use GM mode).

As a general rule of thumb, with older games I use my real MT-32, even if it supports GM, but am not disappointed by the SC88 in emulation mode, with newer games I prefer to use the SC88 in native mode.

I like turtles.

Yes, they did support those custom sounds too.