Maybe intuitive wasn't quite the right word, but it's a few things, like how the message bar at the top of the screen tends to draw the player's attention to itself with large text and flashing colors, while the message bar in the bottom left corner is out of the was, but since the top bar tends to fill up larger than the screen can contain, the bottom set of messages are much more useful.
Maybe they'd be more noticeable if their position were swapped with the location of the player's skill list? Something like
this maybe? The reason being that while both the skills and messages are important information, the player's skills change infrequently while messages change all the time, so the player shouldn't need to reference the former as frequently, and the latter should be given a position closer to the player's center of vision.
I do like the skill hotkeys. Much more convenient than the old mbaa* or whatever it was just to use a basic spell on a target. You don't see skill cooldowns very often in a roguelike, but I think it could work out well here.
Combining commands like read and quaff into a single use command isn't necessarily a bad idea (in fact, I think it might be a good one), but it is unintuitive to a roguelike player since q and r are
always quaff and read.
The game seems to want the player to use their mouse to look at things. While the ability to do so is nice, I would bet that most players would like some way of doing every task with just the keyboard.
Maybe I'll post more suggestions later.