The problem with the 3.6 site theme updating is that a "/" is missing in the confirmation link sent by email, separating "oldsite" from the next word (or the word before...), it can be manually corrected in the meantime
There is very little point working on themes for the old themesite and syntax. There is a good chance it will one day just dissapear (probably around 3.7... so 3 months), s moving your theme to the new syntax and getting everyone onto the current builds is the way to go.
I have to disagree here. While indeed after the next release there will be no point to use the old syntax, I don't think it's reasonable to say that there is little point in making themes for the current release.
More people download the themes from the "oldsite", the total downloads have grown a lot more there than in the "standard" site since the theme sites were split
Edit: the 3.6 site uploading link seems to be working now