First and foremost, the way the sprites are done is a really neat idea, but I think this does affect performance just a bit. I do play on Android, so perhaps it's not that bad on PC and this is just a nitpick, but I still feel that at least a bit more optimization could help.
I do like the time limit challenge it gives, since it's a nice change of pace to the base game, but at the cost of bosses? Not so much. The bosses are pitifully easy when you have homing shots, which are understandable for normal levels so that you can focus on going faster and not have to slow down to aim, but the bosses using this same logic makes them extremely disappointing. Personally, I would have made bosses remove your homing shots to force you to aim, granting you 2 extra seconds with every successful hit but penalizing 1 second for every miss.
I also love that you play as the Flicky inside Gamma for the special stages. That's honestly adorable. It *does* make certain parts a bit harder to hit because of your vastly smaller hitbox, though.
Overall, really nice mod. There's some things that I think make it either disappointing or boring at points, but that's not that awful enough so as to deduct more than one star.