Is there anyway to force game resolution to your native desktop res like you can in CIV3?

Nope, MoO3 only comes in 800x600, you can do nothing to change that. But there are some released changed fonts to improve the text readability. Not sure where though.
:D

Check out the MOO3 mini-F.A.Q. (shameless plug). It has links to places one of them being graphics mod that Lucky is talking about. http://forums.civfanatics.com/showthread.php?s=&threadid=46432