Quite loved the original Cave Story. I'm liking quite a few of the mods/hacks that are being made as well. This one was one of them.
I like the idea of running things through what Might have been if Quote left early, though it probably could have been more fleshed out. For a Retro game though, its good.
As mentioned by some of the others, this was a jumping nightmare. If your no good at the back and forward jump, this game would be quite frustrating, but once you get the hang of it, its pretty good. I didnt really have much of a issue with Save Points. Infact, I really liked the fact that you had plenty of them in the Collapsed area right after the Power House *Ahem...Im not exactly a expert at jumping myself. Reset several times*
I think one of my only true gripes here was the boss battle. The original Doctor was alright, but then you had the Golems which where just reskinned versions of Ballos, and his other forms. At first I was like "Meh, alright. Its easier to use pre-existing attack and movement patterns then coding in your own" but then I came across the other 2. So many repititions of the same kind of battle was more annoying then thrilling. Perhaps, a alteration of the second and third golems Altered Forms would have been better. Either way, it turned into a finger cramp-slowdown button mash by the final golems final form.
But enough of the gripe. As mentioned before, overall I think its a good game with a interesting idea.
Possible ideas though: In the begining, the Hero Mimiga *Forgot his name already >.<* could have had a platoon of the other Mimiga's even transformed, fightinng against the Killer Robots that the humans where preparing to send once more, but after the battle is over, the Mimiga run wild, and the hero's own person best friend attacks him. Just...Idea for any future reiterations of the game. That is, if your accepting ideas, and if there are going to be any future reiterations.