The Game Gear is technically just a portable Master System, so by the same logic Master System games should probably be allowed as well. But they might as well just go all out and offer any sort of game which the 3DS hardware is capable of.
Sure, both systems had very similar hardware which is why so many of Game Gear's games were direct ports of those from Master System. But, each were considered their own separate system, had different specs, and their games were written in their own separate formats. In other words, you couldn't take a Game Gear cart and stick it in a Master System or vice versa. TG-16 and TurboExpress on the other hand, shared the all the exact same specs, and used the same game cards-- they weren't separate systems.
As far as Virtual Console goes, Nintendo has clearly been keeping portable and console games separate-- never releasing any games from a handheld on the Wii's VC, and with the exception of TG-16, has only announced games from portables for the 3DS's VC.
Granted, NEC did release a portable variation of the TG-16, known as the TurboExpress, but once again, it wasn't considered its own system. It simply played TG-16 games, just as Sega's Nomad was merely the portable variation of the Genesis and only played Genesis games.
Today's announcement confirmed TG-16 and Game Gear support. So, so far that makes Game Boy, Game Boy Color, Game Gear, and TG-16-- all handheld-specific formats except for the latter, making TG-16 the glaring exception to the rule. It's clear from the other supported systems that they're trying to keep console games exclusive to the Wii VC lineup, and handheld ones to the 3DS (besides TG-16).
So the question is, why are they making an exception for TG-16, and not others? And since many of us already bought TG-16 games via our Wiis, will we be able to transfer them to 3DS as we will DSiWare?