Just recently put a set of Pioneer 6-1/2's and they sound good. I thought of upgrading the speaker wire, but since the wiring coming out of the deck is small(16-18ga), is it worth upgrading it?

 

The effect of going to a larger wire would practically be inaudible and not worth the expense and effort to upgrade. This is especially the case if you are using the factory deck which only puts out less than 20W/ch.
This site has good info on speaker and power wires...
http://www.bcae1.com/wire.htm

 

Save your money - new wiring won't make a difference.