First let me say that I am in love with WpMuDev, the dashboard, plugins and features are spectacular but the best part is the thriving community. I've learned so much about WordPress and BuddyPress just in the short time I've been a member and I can say that, without a doubt, it has been a great influence on my websites.
One of the biggest issues I've had has been the ability to customize my themes the way I want. I'm not a big fan of using other peoples themes because they will never fit my exact needs. I have purchased Carrington Build Unlimited ($999) and UltimatumTheme ($170) to build themes with a true "drag-and-drop" layout design but the problem with these are they don't really like to work seamlessly with things like MarketPress and Affiliates.
What I would like to see is the boys and girls at WpMuDev crank out their own seamlessly integrated drag and drop wordpress theme builder with the features and functions of UltimatumTheme and Carrington, but wrapped around the awesomeness that is CustomPress.
The biggest issue I have with CustomPress is that I can do the custom post types and pages types easily, but I can't layout the theme the way I want and the widgets and plugins that WpMuDev have.
I'm not sure if this has been discussed before or if it is even a blip on the radar, but I would love to see WpMuDev come out with a full featured drag-and-drop theme builder.