I guess a good question is, would I gain any performance shoukd I choose Linux vs Windows? According to my reading, Emulationstation is on Windows, so if I don't really lose performance by going the Windows route, I will do that, as I have no Linux experience, but if I can gain performance by using Linux, I have no problem learning Linux.
In any case as far as storage, I would take out the included 8GB SSD, and replace it with a 2TB 2.5" drive via SATA male to female cable. I would also increase the RAM to 4GB.