It took a few days longer than I'd like but I was able to implement some new stuff:
Slopes and stairs based off of https://github.com/krix/SlopesTest/blob/master/src/FlxTilemapExt.as
Different background colors, patterns, and decorations (just columns for now)
Different art and architecture preferences for each region
Each region gets a few architecture and art preferences. The architecture preferences are used to determine the room generation: what tiles are empty, solid, or stairs. The art preferences are used to determine the graphics: what do the background, stairs, walls, and floors look like. There's still not much content but I have a simple system set up and I can add more and better art or architecture styles later. Alpha content will suffice for now.
There's still a bug where moving into another room sometimes bumps you to a different space. I can't pinpoint where or why though. It seems to only bump you towards the bottom of the map and never the top. It also seems to bump to the left and never the right. So it bumps up the Y axis and down the X axis.... weird.
I think it's time to focus on player graphics for a while. Since I'm better at programming than art, I think I'll try my hand at skeletal animation. Flixel doesn't have anything like this as far as I can tell but forward and inverse kinematics should be fun and make a lot of the art stuff easier too. I estimate about a week until I have something useful.