The biggest difference, IMO, is that you don't continue where you left off. After losing your last life, if you choose to continue, you are whisked back to the beginning of the stage whereas the AES/MVS versions will allow you to continue where you died.
I guess I actually kind of like this feature, since it really forces me to learn the stages an improve my MS 3 skills.
This game isn't quite as stable as the AES/MVS version either, I guess that should be mentioned. Although it's pretty rare, the game will occasionally "skip" on the flying mission segment of the final stage. What happens is that you keep flying but the enemies stop coming, and you're just left there flying and eventually run out of time. I thought this was just some random error, but multiple people on these forums have experienced this problem, although as I said, it's quite infrequent and really shouldn't deter you from getting this game.+
Overall, I think it's a great port, and wouldn't hesitate if I were you.