Ford's 4.0L SOHC V6 has timing chains in the front and rear of the engine and not just in the front like most OHC motors. What this means is that the engine typically has the be removed from the vehicle when replacing timing chains and guides. This makes the cost of this repair quite expensive running around $2k-$3k and is usually required between 100k and 200k miles. It isn't a matter of if, but when, this will happen. The second is the five speed auto transmissions in 2005-2010 Mustangs are not the most reliable. One problem is servo bore wear due to Ford using the transmission case for the bore lining and not a proper sleeve. The odds of a transmission rebuild is highly likely as the miles rack up over 100k. This would be a $2k-$3k bill to handle.
If you want to hedge your bets then buy a GT with a manual transmission. The 4.6L 3V is a very reliable engine and the manual transmissions are also very reliable. Should it ever need the timing chains and guides replaced then it is a much cheaper repair since all the parts are located on the front of the engine. Also, in the rare case the manual goes out, it is much cheaper (and much more reliable being a manual) to buy and install a used five speed manual than rebuilding an auto. A clutch replacement isn't all that expensive either at around $500-$700.
If you can do all the work yourself then you might be good getting a V6. In any case, I would avoid the auto transmission cars.