I've never owned arcade hardware though, and I've done research on the naomi, and basically it seems like it isn't all that easy to get a cheap or simple setup... even though the motherboard can be found cheaply, for the following reasons.
1) The games, particularly the shmups and the mid-late 2000s era of games that I am most interested in come in different formats (cart or GDrom), and many of the more interesting later games are extremely expensive and rare JPN only releases, and are even just hard to find for sale at all. (Stuff like Karous, Illvelo, Radirgy Noir, Melty Blood, Senko no Ronde, etc)
2) Buying the extra hardware (gdrom drive / dimm / or compact flash) seems to entail several hundred dollars.
3) The different formats, and the different regions games are released in necessitate having particular bios revisions or regions. Ie: various JPN games only booting with a jpn region bios - and the GDrom/dimm/compact flash/netbooting only working with particular bioses (which I don't even know the specifics of, but I assume the naomi motherboards I can find from US sellers for under $100 on ebay won't be stock ready to play many of the rare Japanese games I would like, nor support the gdrom or other hardware needed to play non-cart games, nor play various JPN cart games).
4) I'm a complete arcade noob and don't really understand how you rig up controls for a naomi or what an IO board really is. They seem kinda expensive though.
So, do I have a pretty good understanding of the situation? Basically - you can get a naomi motherboard at an affordable price, but expect to invest an extra ~$200 for the hardware necessary to play games, and another couple $100 per non-dreamcast Japanese game?