Personally, I don't mind the comparison threads. They're mildly entertaining. Just my $0.02
As far as GoT vs. TFIII, it's GoT hands down. You're talking about Technosoft's second or third best shmup (behind TFIV and perhaps Hyper Duel as well) compared to what might possibly be the greatest horizontal console shmup of the 16-bit era. The only other console-exclusive hori shmups that come close to Gate of Thunder are TFIV (very close, arguably equal in many ways), Gaiares (you either love it or hate it), and Lords/Winds of Thunder (not the same kind of shmup, but arguably better graphics and presentation). I would also throw R-Type into the mix, but that was an arcade port, albeit a great one.
Don't get me wrong, I love TFIII. It still stands as one of my favorite shooters of the era, but it just doesn't hold a candle to the towering and monumental Gate of Thunder. Hudson and Red really outdid themselves (and everybody else) when they released GoT. It was truly a landmark in 16-bit era horizontal shmups.