History not working correctly sometimes: people should have told me back during actual beta testing. I knew I screwed up at least one, even though I double-checked it all, but too late for that...
Visual cue for the boss low on health: Check the enemy marker. It changes color and flashes faster when the boss is low on health. I'll add an additional effect to make it more obvious, if you want.
Focused speed: Personal preference, really. When I had Raibys's focused speed low, I found that I was forced to unfocus sometimes to dodge things that shouldn't really require it, which can be pretty limiting for something like Frost Form (which you never seem to use anyway, so it probably wouldn't matter to you). I tried to find a balance, and I'll probably lower it by 0.5, but it's staying somewhat high.
Effect blindness: Yeah, I'll cut down on it. Yumemi seems to be the only one that multiple people complain about, though.
Too many lives: Remember that you also die more often, since lives aren't linked to bombs, so having tons of lives isn't as much as it seems. I mean, in the video you posted, you were still pretty short on lives by the end... Also, the only things that drop pink are the bosses (and one or two individual stage enemies), and bosses drop slightly more if you capture an attack.
I'm trying to go for a "high difficulty but lots of lives" method of balancing, rather than "low difficulty and few lives", for multiple reasons. It makes each mistake less of a blow on your overall performance but requires the same amount of skill overall (same logic for the new bomb system), plus playing through lower stages is more fun when you're trying to capture things you haven't before (as opposed to Touhou, where if you reach the final boss and play through again, the first half of the game will probably be extremely easy with no real challenge).
Art: I'd rather focus on the important things instead of something you see just in dialogue. At least there's more variety in the poses.
Selling the game: it's going to stay free. It wouldn't feel right selling something that's inspired and based on someone else's work.
I love you: I love you too.