1. Yup, fully aware of that issue. A last-second buff to the ice weapon combined with a last-second nerf of the rock weapon kinda resulted in that, since the ice used to be way too weak and the rock way too strong.
2. They're primarily intended as a way to let you gather HP before bosses. Most important in HP rollover mode (doubly so in game reset HP rollover mode), where your hitpoints are carried over from stage to stage (and in game reset mode you start the whole game over if you die once). It was also done to move the focus almost entirely over to the boss battles, in a similar vein to Alien Soldier. It's a good thought that the enemies could possibly be set up to teach you about some concepts that some of the bosses use though.
3. The checkpoints in the final boss were an anti-frustration feature, as there are a few final bosses that I was this close to liking in some games but then they had way too many forms with no health restores and no checkpoints. In other words, I did it because there are some final bosses that I felt were ruined by not having checkpoints between phases. I may have gone too far in the other direction here, mind you, especially since most of those games required you to replay super-long final stages if you even died 2-3 or so times between the boss and the stage.
Overall, those are some fair criticisms you have, maybe I'll be able to keep them in mind for the future.