It is all preference. The footprint of Japanese cabs and US cabs is practically the same. Plus the Japanese cabs will require chairs which increases the footprint. No matter what, they are both cumbersome to move around with Japanese cabs being less so by about 30 inches in height. You'll pay a pretty penny for a Japanese candy cab and they are no fun to work on due to the confined spaces. If you have a row of Japanese candy cabs, any hardcore gamer will instantly revere you. But it is going to set you back a pretty penny. Since you are just getting going, spruce up your 3s cab to your liking. Then as you read more and are more aware, perhaps are even lucky enough to find one to play on, then target getting a Japanese cab for yourself.
Being a stand-up guy, I prefer US cabs. I think it goes well with that wham bam most fun you can have for a quarter and then you're gone style of play that was what arcades were. But again, it is all preference.
Getting back to CvS2, it runs off a GDROM and a Dimm (or a Net Dimm set to run off GDROM). A working GDROM drive will set you back $150. CvS2 will set you back $50-$100. Also, you'll need a Dimm ($30) or a NetDimm ($150-$200) to play it. Add in the cost of MvC2 and that will cost you another $100-$150. You can get a NetDimm, save all those costs you'll be able to net boot and play both games in no time. You sound more gamer than purist so think the Net Dimm option is best for you. The good news is I know of a reliable Internet merchant that might be able to get you a Naomi and Net Dimm for $128 plus about $30 shipping. I don't want lurkers to drive up prices, so PM if you decide this is the route for you. From there, all you need is an I/O board ($35) and a PSU (from $20 to $100) and you're off and running.