Kane, was not what I expected as a final boss. And I don't man that in a good way. I don't mean the fight, or the overall story, (both of which were done fantastically, by the way) but Kane himself was a poor character. The same goes for Queen. Blind Mew, you said it yourself, killing off a main villain shortly after you meet them is bad storytelling.
My favorite kinds of characters are, without a doubt in my eyes, the villains. Especially the ones that I grow to hate. The ones that pop up throughout a story so much it almost becomes annoying how much they show up. The ones that have an grim backstory. The ones that are terrible and atrocious, but beneath it all..... just downright cool. I hope that conveyed how I feel about villains enough, because I thought that Kane had the bare minimum of that. The only thing that made me like Kane as a character was what we were given through Gazpaccio's puppet shows. The idea that Kane was born as spawn of Gazpaccio's own dark emotions was pretty cool, but I wish there was more to him. I tried my best to hate Kane, I really did, but I just couldn't. He was far too lacking.
I also think that Kane's downfall, while likely his true downfall, was too easy. Not the fight, (you did great Ratbeard) but the aftermath. Kane is quite the calculating mind, in fact, his mind is likely a bunch of 1s and 0s. Even if he calculated he had a 99.99999% probability of beating us, he should have programmed some kind of Final_Killing_Blow_Geronimo.exe in the slim, slim case of that .00001% chance of failure. It probably wouldn't work, and we'd have some way to avoid it, but hey, as long as he takes the necessary measures.
Also, Queen was equally as, if not more, disappointing than Kane. Queen was a certain character we truly had no answers about, except that she was Kane's right hand Elite. She was shrouded in mystery, and one of things most debated about was her name. Some of us, including me, made it very clear we did not want her to be named Queen, but something more imaginative. Just giving her the name Queen killed it all. And to add to it, we got nothing more on her. No solid backstory or motives, except from a few lines from Kane.
Now, I know in the end, you decided to close the Kane Arc here, for reasons which I cannot seem to recall, however, I genuinely would like to see Kane return, perhaps in El Dorado, as that may have well been where his Golden Mind went. I really want to see more of him, and at the same time gaining a reason to hate him.
So, finally, I'd like to say that, despite my list of gripes here, the game is absolutely phenomenal, and I can't wait to see what the next story arc has in store for us. Thank you for all your effort.