I'm on my third GG, and like the others here, I hesitate to call them quirks, but here's my list.
Kickstand. It tucks away really nice, but the auto retract is uncommon to us here in the U.S. Quite frankly, I still don't like the auto retract. On my first GG I moved the spring attach point on the frame and solved that problem. Since then I have not bothered. Although I have broken no less than 5 kickstand springs.
Carb: This is an odd one. I went to put on a Power Now gadget... You know, the one that puts a little wing inside the inlet. Well, I guess not all PWK 39's are created equal, because when we pulled one out for a KTM with that same carb, it didn't line up with the holes. Wierd. The positive thing, my 300 doesn't need any help.
Throttle cable: I saw it here before, but with my sub mount steering damper, a longer throttle cable is a must. Sub mounts weren't even available last time I owned another brand, so I would assume I would need a longer cable with them as well.
After market goodies: Some products just aren't made for the Gas Gas. I want some of that anti slosh tank foam. They make a universal fit, but it sure is nice if it's been thought out directly for your application.
All of these are tolerable things. It's way easier to live with the Gas Gas than a converted Japanese MXer.
A side note about quirks: Some quirks would steer me clear of a bike all together, others are a pain. With the GG, there is frankly no real pain in the rear.
I had a friend with an ATK 250 LQ once. That bike was a project. After gusseting the rear brake reservior, rethinking this and that, and figuring out how it all went together, that bike worked really well. It was fun to ride, and easy to work on. It did, however take several weeks to sort it all out when he got it. Right up 'till the first time he broke his foot between the shock and whatever. Apparently it's easy to catch your foot on that shock, because he did it again, twice before replacing the bike.