I swapped out my MVS collection for AES last year and definitely don't regret it. Most of my favorite Neo-Geo games are of the early 90's variety (the ones I actually played in the arcade as a kid), and those games can be had pretty cheap. The most I've paid for a game was $110 for a mint copy of KOF '98. The second highest was $45 for Crossed Swords. It's really not that bad.
Once you get past about 1994 or so then you're really talking bucks - obviously the biggest culprit is the Metal Slug series. There's always the MVS-converter cart if you gotta have Metal Slug on your AES.