There is no practical ballistic difference between the two. The receiver difference is about 1/2" shorter for the .308, which translates to a few ounces of weight at best. Availability of commercial ammunition for either is a non-issue. The CMP will be getting another huge supply of surplus 30-06 so price of ball ammunition should favor the 30-06.
So the bottom line is that for a few years ball ammunition should be cheaper for the 30-06. Reloading would mitigate even that. The only other thing is that no military type semi-automatics are made in 30-06 while a few are in .308. And if that doesn't affect your choice, buy the best value for you. Also, if you are desirous of a military surplus firearm, the 30-06 wins easily there.