Plants that are more resistant to herbicides/pesticides (weeds/bugs) due to GMO is my main gripe. Indoor growing and hydroponics is the best solution to this from my point of view. I have no problem with making food more nutrient-rich via GMO. I am well aware that all foods get sprayed, I'd be nice if none needed to be used and plants didn't get modified to make their own herbicides/pesticides.
I'll probably anger both side of the debate because I'm not 100% on one side or the other.