First thing first, the loading times are way better than the ones in Real Bout Special. Also, there is a real VS. mode as well as a survival mode if you're into that but that's pretty much all the positive sides of this version.
The rest of it... Well, how can I put it... It's pretty meh. Yes, they had to cut some animation frames whatever Gamefaqs is saying (just a few though, Laurence comes to mind) but they also ruined the kick ass original soundtrack with a bunch of uninspired remixes. They cut all the crap from RBS in RB2 to make it a very fast paced and intense game. The loading times of the CD version are totally ruinng that. Seriously, this is the worst version of Real Bout 2. There is no point in getting the Neo CD version anymore now that you can get it on the Wii and PS2 for pretty much nothing.
For real, do yourself a favor and play this masterpiece on proper hardware (MVS would be the best but you know that already). If you're broke, get yourself the rom on the Wii, it's pretty much arcade perfect with no loading times whatsoever. It's like $9 if you don't have a hax0r Wii.