Well, they all have their pros and cons. Here's a breakdown.
NeoGeo CD/CDZ - can play Backups, games are pretty cheap. Load times are unbearable. Close to 60 seconds for ONE MATCH in King of FIghters 98. (thats IN BETWEEN ROUNDS TOO) To me, not worth it.
NeoGeo MVS (arcade) Most bang for buck, for older games. KOF98 can be found for as little as 25 bucks, while new games, like Rage of Dragons/KOF 2001 can run about $700 to $900. Great for getting older hard to find games. Bulky. Decent value. Games decrease in value rather quickly.
NeoGeo AES (Home Cartridge System) - Best Value. Games are evenly priced, older ones (Magician Lord, Samurai Shodown 1, etc) are in the 30s, to 50s. New games, can go as high as 400+, more if they are in limited issue.. which 99% of them are. Games increase in value over time. Metal Slug 1 can be over $1500. KOF94 can still fetch over $100. Carts are prettier, have casing, manuals, etc. Nice for a collector. Irrelavent for a gamer. (they are irrelavent to me)
Hope this helps.