I would go with the 6-in-1.
The NAOMI setup is pretty expensive by itself. The games usually aren't cheap either running $100 plus (according to eBay). I lucked out and got mine in a 25" cab on the cheap, but I haven't been able to drop bank on the GD-ROM unit to increase my selection of games. The GD-ROM units sell for more than I bought my entire setup for. :-/
Even though the NAOMI hardware hasn't been emulated, the games have been ported to consoles. Those consoles (Dreamcast) may be emulated. I thought about this for the CPSIII since it too has not been emulated, and probably never will be.