Wow, looks like there's a big discussion going on... I must say I agree with blackadde, what he says is perfect common sense. But BlackSpy is also right when he says common sense doesn't apply here in this site, I've also tried to preach that type of common sense here in the past and gave up.
About ports, you are right that all the Neo Geo ports up-to-date are INFERIOR to the real thing. The Neo Geo hardware is very different to any other console. But personally, I think that the Atomiswave can be handled more than OK by the DC (basically is the same hardware), PS2 and also GC and Xbox (but it looks like PS2 will get most of that ports). About loading times, nowadays they are minimal, it's not a NGCD (which by the way is a SNK made console). Also ports usually have more game modes more suited for home use, among other extras. Plues ports are much cheaper and have amjor market, so they are actually profitable.
About the "true arcade experience at home", well, sorry to wake you up but I don't see the AES being arcade perfect. It's not the same playing in a TV with the controller in your lap that with an arcade cabinet in an actual arcade place. So the only true arcade experience is getting a cab (you would still miss the atmosphere, though). In my case, as much as I like arcade games, I prefer to play them at my home in a console-like environment.
About making a cart-based perfect Atomiswave, I still don't see it being profitable. If you really want it, just buy the actual arcade board, it's pretty easy to use it at home (I'm actually considering buying one), so you just use the arcade carts. By the way, it wouldn't make sense to release a home console that used the very same carts as the arcade, as that way arcade operators could get the "cheaper" home versions. Just think why SNK made the MVS and AES games being incompatible, although in the end actually people wanted to do it the other way round (MVS games at home).