I have had both cars that you are looking at. I bought a Legacy 3.0 2 weeks ago, and so far I love it. The engine is bullet proof. I also bought it for the lack of mods available. I got the bug last year for my Legacy GT and didn't see an end. I loved modding it though to be honest. The 3.0 is super smooth and has a terrific sound. I will say it doesn't feel quite as "eager" as the Legacy GT at times. But I will also say that the Bilstien shocks make a nice smooth, firm well handling ride on the 3.0 vs. the GT. Also, the 3.0 comes with 18" wheels, and that made a surprising difference over speed bumps and other bumps on the road. Also, a 3.0 is a little less expensive on maintenance, because it has a timing chain versus a timing belt.
As for the GT:
I had an '05 Legacy GT and loved it. It didn't have any major problems. I drove it from 50,000 to 127,00 miles. The only things that broke were the interior blower motor, and the radiator cap started leaking at 130,000. I replaced the starter as well, it was getting noisy in cold weather.
So I guess it's a choice. Little to no mods, but a nice smooth ride. Versus, nice quick speed, the option of a manual, unlimited mods, and a larger following. There are not a ton of 3.0R people out there. Either way you will be happy especially when you find a nice road. The only difference is wether you car will have a turbo whistle or the groan of the flat 6.