I don't like the random bosses just because the hard dungeons all tend to have a fairly specific theme going on, and the random bosses nearly always clash with that. Although I do like the gold reward for penultimate boss kills. Maybe secondary bosses should be specifically assigned to dungeons that suit them? That would also help with trophy hunting. And, yes, at this point I think it's indisputable that Bleaty is broken - you can't even rely on CYDSTEPP to beat him anymore. Lower Bleaty's mag resist to 0%, and even then he's still somewhat overpowered; while you're at it, give Tomithy and Medusa probably double the HP (or give them Bleaty's mag resist), although that doesn't quite bring them up to par either.
I've only seen the dialogues on my main profile where the vicious Tower is already beaten, but from the sheer number of them I'm going to say that I think the Horatio quest line takes way too long to get going. Maybe it's not as bad if you're playing from scratch, but having nearly the exact same dialogue come up several times in a row, with no noticeable change in the game state, seems rather tedious to me. Just start the quest chain later if it's going to take that long to get going.
Have treasure subdungeons become rarer now? I hardly ever find them anymore. Considering what a huge power boost those are (particularly on Purist runs) I think they should either be more common (if harder to access) or there should be other gimmicks that replace them if one doesn't spawn. Right now they add way too much of a luck factor to a game that already has IMO too much emphasis on luck (and/or scumming, naturally).