Great. Just great.
People install into Program Files (x86), people complain about games not working.
install into Program Files (x86), people complain about preference issues.
I guess the next logical step is for GOG to disable UAC automatically with the installer. Oh, I can just see the virus alert topics sprouting up.
In all fairness, I've encountered several games over the years that ONLY work when installed to Program Files. So if GOG were to start selling such a game and you couldn't install into that directory, then it's a bit of a problem.
For example, on some non-English language versions of Windows, Spore could only patch correctly when installed to Program Files. When installed anywhere else, it had the tendency to bugger up.