If you can afford a 05+ v6 then just grab a 99-04 GT for cheaper. Is a lot more fun too.
But to answer your direct question, both are reliable engines. I had a 99 v6 and it was a trooper. Bought at 116k and sold at 150k still running strong. All I had to do during those 3-4 years was a clutch (it was manual) and spark plugs.
The 05+'s I hear are pretty good too, and a tad bit faster than the 99-04's... But even they need serious bolt ons to keep up with a 99-04 GT. They are pretty, but if you aren't getting the premium with the nice stuff on the inside (shaker, mycolor system, etc.) then it's not that much better than the 99-04 interior.
On looks, the new edge rules. When you see a clean new edge with the right mods, your panties will drop and you'll forget about 05-09 body style.
Mine doesn't even have any exterior mods really. Lol
Yes I edit my posts a lot, auto correct likes to sabotage me!