In the newest revisions, the micro VU recompilers appear to be their own option, not positioned as a sub-option of the standard VU recompiler (now called "Super Recompilers"/legacy), so I can assume they'll eventually replace the older ones.
I notice they seem to be a bit more accurate, but a bit slower. The differences don't seem drastic, but I assume there's a few games that are quite a bit more accurate/quite a bit slower as a result. I would wager some are even "fixed" from glitches, bugs, or maybe even crashes, with the new micro VU recompilers.