My advice:
If youre dead-set FOR an AES, get the cheapest most beat-up system you can find. Even if its cracked, broken, stepped-on, no controllers/hookups, no games, whatever. Ask around different forums/communities for what the most common games are. Scour eBay and the second hand market for cart-only games (If $$$ is an issue, then cases and instructions are out of the question as they only increase prices).
Alternatively, go the MVS route - your options are much more varied:
-If you have an arcade cabinet that uses the JAMMA standard, do some research on how to wire it so that you can USE the MVS motherboard without shorting out your power supply
http://www.hardmvs.com is a great site for that info.
-Buy a consolized MVS. These will run you anywhere from around $200 to around $400 depending on the quality and options.
http://www.jamma-nation-x.com/jammax/ is a great place to look. Xian Xi (from the NG.com forums) is an absolutely indispensable resource for CMVS stuff, and his work is always top-notch. Options (memory card slot, video connections, bell and whistles, etc.) will affect the price, but I also know that he wont be building CMVS's for very much longer. JNX is not the defacto standard in buy a CMVS, but its at the top of the list for options on where to get them.
-Build one yourself. With a little know-how and some research, you too can build a Neo-Geo. You would still have to source the motherboard (stick with a 1 or 2 slot, as anything else, so I've heard, can give you some trouble once consolized), but they're much easier to locate than a cheap AES. My advice, for what its worth, would be to get a two-slot board and follow the step by step guide on jamma-nation-x.com. Once again, indispensable.
When buying MVS games, stop the madness here and now and DONT USE EBAY AS A PRICE GUIDE. Forums are much better, IMO, because its an established community of PLAYERS, not flippers, scammers, hoarders, or resellers, and prices are more akin to a games ACTUAL worth as opposed to what its worth RIGHT NOW (and you also gain some knowledge on who to AVOID when buying games). I like the early releases myself, and they just happen to be the more cheaper, common games, and they STILL play better than anything that's come out for the modern consoles.
Parting shot with MVS:
Get a UniBios.
Switch it to "console" mode.
You're now playing an AES game.
See how easy that was?