Skinning was easy for me so far. I personally just edited all the main View files instead of the theme folder. I only did this because at first I couldn't get the theme folder views to work. (To fix that, just copy over the web.config from the
real Views folder to the Theme folder.)
For the upcoming releases, I'll move back to the theme folder just to keep with good standards. I'll also have to put all my custom code in plugin format. For now I've been just adding my own controllers and such.
I also need to see if I had any other fixes for you. I know I posted a few on the mesoboard forums, but I think there were a few more. If I can think of them I'll let you know.