Yeah, Lightening Force definitely wins this one. All three are fantastic games, which makes this a tough competition, but Lightening Force is my favorite Genesis shmup, and it takes a small edge here. Aldynes definitely makes me want a SuperGrafx sometime, though...
As for Super R-Type, I like the game -- it was the first shmup I got when I got my SNES back in '05, and I actually finished it, something I still haven't managed with R-Type on TG16. Sure, you restart the level when you die in Super R-Type, but you have unlimited continues, so I could just keep trying until I got each level right. In TG16 R-Type, you have to restart the whole game after about 15-20 continues (using the code for extra credits), which just is too few -- I can't beat R-Type on so few continues, I always run out somewhere in level 5 or 6. The version of R-Type I've managed to finish is the GB/C version (R-Type DX, which is R-Type 1 and 2), which has a level-select which saves which levels you have unlocked and infinite continues. Also it only has 11 levels, since three were cut from those ports. It's a really great game though, on any platform. The first R-Type game probably is the best R-Type one... the sequels are good, but the first one set the standard. Still, R-Type III is great, and in most ways is a great improvement over Super R-Type, with less slowdown, better graphics, and more.