I think its controls are fine; what understandably puts off some people is the level design. In other words, the controls are very well suited to the gameplay, but the gameplay itself is so weird and defiantly stodgy that some people never get into it. The game is very strictly tile-based, even when you aren't literally standing on a tile, as Mike always moves per unit of space. Many enemies, like the snakes, are carefully placed to interplay with Mike's movement abilities. Off the top of my head, I can only compare it to the Lolo series. Then there's the jumping -- it is certainly not used as you would in a side-scrolling platformer. You can jump to dodge enemies, but since Mike goes straight up and down, the timing is pretty tight. When on tiles, you have to look ahead one or two moves and also try to match your jump timing with that of nearby enemies. Also, one vital and non-obvious technique is that you can change direction in mid-air. It won't change where you land, but it does allow you to attack enemies in mid-air if they pass by you on a parallel trajectory.
I haven't played StarTropics 2 in a very long time, but I distinctly recall feeling that the smoother controls no longer matched the gameplay, so it always felt off. Of course, I'm not opposed to smooth controls on principle, but it seemed like the level designs and combat were left alone, while the controls were changed significantly, and that left a rift that never felt right. I would be interested in giving the sequel another chance, though. Yet another one for the NES follow-up poll!