Planning on paper works really well. Yes, even when you plan random generated levels. It's easier to think what types of rooms or other features you need in that level theme.
Of course I ran into problems when a new shape for specific type of room was needed. The way walls are created works only for rectangle shapes and it's possibly difficult to fix so I'm doing it the easy way with blueprint tech developed for Teemu.
I also came to a conclusion that it's simply impossible to create all level themes with a single routine and data input. It's not that bad, I just need to write routines for each level theme using tools that already exist. That way I can do all types of funny stuff to create special themes. The order of creation plays an important role here, because changing the order makes funny level themes possible.
Another big thing is also the amount of randomness in some level themes. I was thinking that a long time and wondering how I could make level themes random enough. It's not the issue really. I could make endless number of variations or then I could start to finish level themes and make them less random. If it's creating too static themes I'm changing the game from a roguelike to RPG with save/load game and removing permadeath.