Can you have tokens that represnet Large or larger creatures?
Absolutely. By default tokens fill exactly one square. To change that, select the token (or tokens) and right click on it, pick the Size menu, and select the appropriate size.
Just tried it and man that is great. Is there a feature in the works to show threatened squares?
There isn't an official tracker for threat squares scheduled for the 1.0 release, but we have already talked about implementation and expect to include it in a post 1.0 release.
For information, we expect to release M5 to beta within two weeks which will freeze feature additions, then have an M6 for usability cleanup (let us know if you have usability preferences), then release 1.0.