I chose MD over MP3 though mp3 players do have many advantages.
MP3 pros
-no skipping (no moving parts)
-small
-fast transfers
-lighter
MP3 cons
-not as mature as MD technology
-limited to smartmedia

(this was a big one for me)
-listening to the rio300 (crap), but the rio600 and ipaq are much improved in terms of sound quality.
MD pros
-cheap minidiscs
-haven't skipped yet
-my sony mz-r90 came with a stick remote, very important.
-newer stuff tends to be smaller/same size as most mp3 players
MD cons
-not as easy to use (i had to buy sound card w/ digital out for best sound)
costs are essentially gonna run you 200 dollars going for a newer model of mp3/md player/recorder so its your call...if you have a short attn span, MD is the way to go. If you like to beat the same songs to death over and over or you don't mind loading songs b4 class every morning, MP3 may be the way to go.
things to consider
-headphones that come with the units usually sux.