So, I'm going to come out and say it: I was wrong about this game.
Now that I'm playing it in English, and some of the complexities around the stories and ideas are making more sense to me, I rather like it. The presentation is a little like Nier in the sense that it's very much like an opera. The plot is deliberately vague and subtle, charaters are tragic and there's a violence to this game that's quite transgressive. It's nothing like Castlevania in that sense: that series is as generic as they come. Pandora's Tower is at its best when it isn't being a game.
Of course, it still plays terribly. Really, really badly, stupid pointer controls and all, but as an experience there's a dark beauty to this game that puts it above the far less original Xenoblade (JRPG take on Skyrim? I'll just stick to Skyrim) and The Last Story (sorry buddy, but you can't out-Final Fantasy Final Fantasy)