As a neo-geo guy I want to clear a few things up from this thread.
1.) If you go MVS, try to avoid 4 and 6 slot boards. They are notorious for issues, especially the 6 slot boards.
2.) MVS is going to be all around cheaper and give you more options but requires more 'up-keep'.
3.) They make MVS to AES converters for playing MVS carts on the AES, but are fairly expensive and not compatible with some multicarts.
4.) Multislot cabs and multislot boards are NOT JAMMA, but a variation that has stereo sound. Only the single slot boards, and cabs are JAMMA. Some single slot boards however are capable of outputing stereo via a header on the board or a 2.5mm headphone jack.