If you are gonna use an ArcadeVGA, not really, in that case, if you can't opt to have no graphics card, then go for the cheapest or one you want as a spare for anything.
3GBs is fine for most games, but keep a mind for future. I believe the biggest Memory usage is probably Naomi-GD games (that work anyway), since they use about 1.2~1.5 GBs of memory *prepares for dev*. But other than that, should be fine.
640GB is fine for now, but again, make an idea for future. If you are like me and download only the ones you want to play, then that's fine, but if you want the whole collection, maybe a bigger space again for future.
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On a quest for Digital 573 and Dancing Stage EuroMix 2