Yeah, you really need to work on the difficulty. I figured you just hadn't tweaked the challenge right, but when I got to the space invaders section, right on schedule, at level 8 it went from almost tediously easy to suddenly ridiculous. That 'too fast to hit' thing that happened in the original game with the last alien happened with the last *eight* aliens. Old fashioned arcade games were hard, but they generally eased up their difficulty at a steady rate, they didn't lull you into a false sense of security, then mug you for all the quarters you had left.
I appreciate the callbacks you did. I like, for example, that you coloured the invaders screen as though there were three different cel tints on a black-and-white screen, so your shot changed colour as it sped up the screen. That, sir, is an old-school reference.
But I think you should consider that a flash game is usually one well-developed mechanic. With three mini-games (I never got to the third one, but you describe three), you've essentially made three flash games one third the quality of one you could have potentially made. Focus on one thing, and you'll end up with a better experience. Tune the game so it's actually fun, instead of throwing in random-ass poison gas until it's sufficiently difficult at a predetermined stage.