Haha.. that's funny you say that, because one of the primary reasons I built a dashboard for SS3 was to break away from the antiquated and annoying site tree paradigm! I was actually really disappointed to what a strong presence the site tree continues to play in SilverStripe 3. I can't stand that thing.
Another idea would be to create a Site Tree dashboard panel that shows your entire tree, with some fancy AJAX behaviors for loading children like the site tree does now. I'd much rather do that, I think. Each panel is a full stack MVC, so all the tools are certainly there to do it.
Hmm... now I'm tempted to do it.