The most recent Sega units by ATGames are emulated, and they do an absolutely terrible job. Many of them have the FM sound channels out of tune with the SSG sound channels. It's a great way to get a terrible impression of the games offered for it.
The older TV Plug and Play ones, however, had a Genesis-on-an-ASIC, a native licensed silicon clone of the original chipset. These were super accurate, and could even have a cartridge slot wired to them by the enterprising modder. They ran at 3.3v, though, so things get quirky with a real cartridge without proper transcieving logic.
Another difference being that the Genesis one is a licensed third party.
The genesis one is pretty bad quality and while it has some good games built in there's lots of not very good one off third party games the creator built in for increased gamecount.
1- Sega went for a "clone" rather than emulation (even accepts Genesis cartridges)
2- Nintendo's IP in the classic gaming space is unmatched
[1] http://www.gamestop.com/genesis/consoles/sega-genesis-classi...