Levels

if you use a file i think you can rearrange levels easier

maybe some combination of the three, plus this?

I guess I’ll just go with the text file, then. It’s the easiest to implement, offers text editing if desired, and is easy to support in an editor. I do like the idea of having a graphical means of editing maps, so that could be done later on.

Yup, save it as a text file.

I definitely would love to see additional layers, at least 1 or 2 extra layers above the floor layer. This would keep from having to use NPC objects as often to place graphics which tend to load slower, especially on slower connections.
Also I would love to see the ability to use alpha transparency in the tile sets, otherwise the layers idea really wouldn’t have too big of an impact.