Not much of a difference. It's more of a personal choice as to which one people choose. Personally I like Borla, and they offer the Million mile warranty, but like I said, it's personal choice. The sound is very identical, with maybe a slight difference, which is probably just because of the different tips.
According to the FRPP site, the GTAs are 50 state drive-by-noise legal, while the 5GTs are only 49 (they lose California).
The GTAs have 4" tips, the 5GTs have 3.5" tips. If memory serves correctly, the 5GTs are the same as the Borla Stingers. Apparently the 5GTs also cost $200 more MSRP....
Edit: Oh, and the GTAs are 409 stainless and the 5GTs are T-304 stainless. Not certain on differences though from the FRPP site, the GTAs apparently will form surface rust that prevents through rusting.
Borla Stinger = FRPP Stinger. Its the same exhaust. Borla Manufactures for FRPP. Only difference, one has borla stamped on the tip and the other has ford racing stamped on the tip. the FRPP is cheaper since its sold through Ford Racing.