The reason Nintendo would pick Konami's NES version of Twinbee for 3D Classics treatment is pretty easy to guess: like Xevious, it features both aerial shooting and bombs that can be shot at the ground, and having the action on these two planes is a good showpiece for 3D effects. What's a little harder to understand is that, while every other 3D Classics game has been updated for the 3DS's widescreen display, Twinbee is in the original NES aspect ratio, with a border of red curtains.
Maybe this is some kind of emulation with added 3D, instead of a full remake like the other games. Maybe the enemy patterns would have had to be moved around too much. Or maybe somebody got lazy.