While the game overall would normally seem like an from previous entries, there are so many bugs in it and generally un-fun elements that it just kills any chance at redemption.
First, there's the fact that if you miss any cards, for whatever reason, and have to go back, you will have to replay every stage after and re-earn every card that also came after that. Okay, score one for realism, and makes it perhaps feel a little old school, but I don't see many games that do this these days, and it's usually frowned on. Case in point, see above game. Second, it won't recognize it anyway. The card is still not click-able, presumably missing. So there's a waste of time. Another is controls. There's no point in having multiple types with this kind of platformer: it has to be WASD + mouse, unless you're just being considerate of south paws, in which I say you need to move the Restart key a little farther away to avoid some potential rage situations. That's not to mention the absurd amount of backtracking and (possibly) rage inducing cheap deaths, in conjunction with the fact that you can't even tell what kind of damage you're doing to bosses some times. Let's face it, unless you're playing a boss whose strategy changes as you do damage, you're left to wonder if you're doing anything at all. This was a huge case with both the Cold Wizard and Gumdrop Machines (or whatever they were called). It's not like I can just type "throw thermal pod" and be done with it. I couldn't tell if my shots were doing any damage at all, honestly, and in the case of the latter, how the hell was I to know that it required a different approach entirely? I spent several minutes trying to take those buggers down, not just because the only clue is infinitesimally small, but because accidentally pressing left and getting nailed meant I probably wound up--like so many more easily done checkpoints before it--throwing myself off the platform to the left of the checkpoint before I realized I was even dead, and having to start the stage from scratch all over again. Gamer's rage, flame on. That's just plain damned rude. Ofc, that's not to mention the sound those things make when they go down (and then waiting for the other one to kick it too). That's horrible too. As if the absence of music wasn't bad enough. Okay, I can bring up my own playlist, yeah, but you could at least try. And if not, what's wrong with a mute option? Or perhaps a couple, one for music, one for SFX? These are the kinds of things pretty much every game should have anyway. I can see from the author comments you made a little effort to improve the game after the fact, but it's still waaay off.
Oh, and finally, that villain mode is horrid. I haven't really played it much since the first stage is so insanely stupid. It's not really worth including if the character you play is close to impossible to work with. Perhaps you have the others in there as a reward for surviving that first stage, but you have to wonder if people are really going to bother unless you're really giving them something to take home for it....
Speaking of which, not everything need to be a hidden trophy, you know. Pretty obvious that one is a game complete, although it didn't work at all while I was playing. Beat the last guy three times, and... zilch. I eventually closed the game and window, then it somehow eventually awarded it outside of it. That makes no sense. Good, cuz I was thinking about taking it to non-working medals. If you're going to put these things in, you should make sure they work right.
Well, I suppose that's enough. Hope that sinks in. If it doesn't, well, good luck. You're gonna need it.
 The star is for listening to people and applying fixes, mostly. Not everybody does that, and that does impress.