I think there are a few ways to divide the series in terms of quality. In terms of porting, they're pretty much all perfect, so the question is which ones go above and beyond the call of the duty.
Afterburner II and Thunderblade are probably the ones which have the most significant new content with their special modes. So if you're looking for new stages and stuff like that, nothing else in the series compares.
Super Hang On, Fantasy Zone, Outrun, and Fantasy Zone II all have extra content which is mostly a twist on existing content without major changes in design or stage patterns. Still good stuff, but it's more about replayability than a whole new thing. Space Harrier has an extra boss iirc.
The rest are pretty much perfect ports without any sort of substantial extras. But in terms of technical showcases, Outrun (60fps!!!!!!!!!), Afterburner II, and Galaxy Force II stand out the most. Thunderblade probably will too, but since it's not available outside of Japan I haven't seen it on a 3DS.
The Genesis titles feature pretty nice 3D effects on the parallax layers, but that's about it. How much you enjoy the titles will come down to whether you like those games to begin with.