Looks like a great project based on the gamedev.tv turn based strategy course!
Overall a clever idea and decent implementation. Some noticeable bugs with screen resolution ("busy" markers don't always cover the "end turn" button) and a bug in "skill shot" locked up the game for me. I also had a hard time knowing which units still had action points. Maybe a "next available unit" button would help with that.
The trooper models are really professional looking! How did you make those?