I happen to own both, and have so for a good while, so I have skin in that game. And I love both.
My 2013 GTS300 recently turned over 40,000 miles (bought it new in 2014). My 2005 GT200 is closing in on 55,000 miles (bought it used in 2010 from the original owner).
In comparing the two, from a reliability standpoint, my GTS is the better bike. Both have been well maintained over the years. Not ridden hard, but regularly on both short hops and trips of up to 2,000 miles. At 40,000 miles, all the GTS has required (other than the usual tires, belt, fluids, plug) is a new variator, a new coil wire and two muffler swingarm bearings. In the first 40,000 miles on the GT, besides a broken variator, a bad ignition switch, a bad starter Bendix, and worn out shocks, a part broke in the carb and went through the engine and I had to go into the motor twice at 36,000 miles to make it right. Not to mention vacuum lines constantly needing attention.
So while I love my GT, the GTS has turned out to be the better bike. At 40,000 miles. At least in my case. We'll see going forward.