As someone who started MVS then sold everything and converted to AES, I can say without hesitation that you should either:
1.) Get a pre-built CMVS like the Omega
2.) Bite the bullet and buy an MVS 4-Slot cabinet (or a 6-slot if you find a good deal)
If this was six years ago I might tell you to go AES but the prices have just gotten out of hand. Even the common games are trending north of $100 each. For comparison, six years ago you could get Magician Lord, SamSho 1&2 and some Art of Fighting games as a package deal for $100...hell my initial AES setup with system, 3 CIB games and a controller was $150.
Anything sought after for the AES (Last Blades, later KOF's, Metal Slugs, Garou) are damn near unattainable unless you shell out some serious coin. Which is silly when those games are easily available on other platforms or on MVS for a fraction of the price.
The one thing that I will say is that the AES looks sweet, the game boxes/carts are badass and the system is very easy to mod (I did S-Video / AV / UniBios self-install with very little experience at the time).
MVS cabs though are really where it's at - it's the format that the games were intended to be played on and frankly it's one of the best arcade cabinets ever made. I slammed quarters into those things for years and years growing up.