You've pretty much got what I'm thinking. The Plexi table would have wow factor, but also a wow that's ugly factor. I'd like a regular looking piece of furniture that also happens to play games...
As for the false bottom, that's the sort of thing i'm thinking. Maybe a pullout drawer with the PCBs all on it.
What I'm thinking for the control part is a false front panel like they use for storage in front of your sink....here's a link sink front tray idea and hardware (http://www.rockler.com/ecom7/product_details.cfm?&offerings_id=58&objectgroup_id=521&catid=81&filter=Drawer%20front) and a picture for ya.
(http://images.rockler.com/rockler/images/63149-md.jpg)
Then inside the table, build a framed box inside to hide the controls when they are flipped up.
I'm glad you brought this up! I hadn't really thought too much about it other than to build a coffee table with a long cord snaking out of it to the TV, and this idea is SO much nicer!