Emilio Lopez:
Looking at #XMen97 to my eye it looks like it was rotoscoped from CGI? My guess is a lot of it was animated in cg , exported and run through the 2D ink paint process and cleaned up by hand with some shots and faces redrawn. Keeping the imperfection of hand drawn art.

Jeremy Polgar:
@EMannLand YO Emilio! You nailed it. MIR did about three sequences in ep01 using this technique and this is one of them. However, this method is almost entirely removed by ep03 and beyond. About 99% of the show is traditionally animated