04+ (esp 06+ with all the nifty little chrome trims, lol) GPs are way nicer and much quieter inside, fewer creaks and such... and as Red said, older car (99/00, ect.) vs 04+ probably be a little more maintenance just due to the age. And, 6th gens have a lot more rust issues/rust prone than 7ths - if you live in the salt belt that could be a concern. I'd never get another 6th gen to DD, but that's just my opinion.
04/05 still had plastic intake gaskets, many of those have been replaced, but not all. 05+ had the aluminum oil pan I believe.
And with the 04+ S/C you get the GenV M90 which makes 20 more hp stock, so there's that bonus too.
As far as tuning, 04s and I believe 05s are easily tune-able, and some 06s you cans swap 05 PCMs into.
IMO, if you can get an 05 PCM to work in an 06 - 06 would be the best overall year. Aluminum subframe and oil pan, metal intake gaskets, black interior w/ white stitching instead of pewter, chrome trimmings, nicer rims (IMO) - harder to find HUDs than 04/05s, but easier than 07s.
If you have a preference for some of the 'rarer' colors - Polo Green was only offered in 04, Fusion Orange was 04/05, Burmuda Blue was 05/06, Midnight Blue was 07/08 only.
Hope this helps ya out. :th_thumb-up: