The unusually easy levels and hard bosses were admittedly intentional as the game is a spiritual successor to Alien Soldier, which did basically the same thing, even if I know it limits the appeal a bit to people who aren't fans of that game.
Though in fairness, this game and Alien Soldier aren't the only two games I know of that purposely put most of the difficulty into the boss fights. Metroid Prime did something like that for example. Love that game too btw, though it wasn't really inspiration for this one, and the reason it did that is quite different since that one was supposed to be about exploring, so bosses being the only hard part just kinda made sense.
Though uh... this one maybe kinda didn't put enough into making the stages actually interesting, which I feel is a much bigger problem than the stages being too easy compared to the bosses. If I make a follow-up, more than making the stages harder, I at least want to make sure they're fun. Fun is the priority, if I can get that down then I feel like it'll help out a bit, heh. That and having more difficulty customization that specifically applies to the bosses, that's also something I've had in mind.