As I logged in the first time in wordpress.com I was a little bit disappointed that I can only choose one of those themes and that it is not possible to customize them. I spoke with some other people I have invited to wordpress.com and they, too, were disappointed about that point. But I understand your problem with that.
But I agree with Joni on this point. The people I spoke with just want to edit the colors of the page and some standard things. They don’t have a clue about PHP and they don’t want to take care about that. They are used to xanga and other services where they can adjust some elements of the pages without thinking about the code. If someone wants to play around with templates in the source he has to install it for himself on a server.
The most important things for most of the “standard” user out there are in my eyes:
1. Change the header Image
2. Change the colors
3. adjust the elemtents in the sidebar (the order of the parts there, what shall be activated, display link categories or make it just a big blogroll [some of the themes do it one way, some other do it otherwise. So if I want to display link categories I eventually have to choose a theme I dont like. Unify it and many people will be thankful])
and 4. If you don’t allow customizing the templates in the source then include many themes, and especially many different themes (not just the standard “sidebar-content” “content-sidebar” layout, but some other kinds of blog layouts), and this would make most of the users satisfied, I am sure.
But as I have followed the discussion about wp.com on this point correctly, then your are on the way to make it similar to what I descrided here. And I think this will solve most of the problems.
Wpmu is a great piece of software. Your are doing a good job on that and I am sure you’ll find a good solution for that problem.