Hi lex. Glad to hear you're looking for a GT!
The only recurring faults reported on here regarding the GT seem to be:
The boot rattle is somewhat erratic, and seems to affect some models a lot, and others not at all. The only way to tell is to take whichever GT you're interested in for a good test-drive over bumpy roads - don't let a dealer fob you off by only allowing you to take it down roads you could play snooker on.
The electric windows have a habit of 'forgetting' where they are. The GT has rimless doors, so the windows should adjust themselves as you open and shut the door to form a seal with the roof, but they don't always do this. Other windows misbehave by not going up or down all at once, or the one-touch function not working. Resetting them often cures these maladies in the short term, but they tend to come back.
Other than that, because the GT is developed from the 156/147, it's benefitted from a lot of the problems on those earlier models being ironed out.
Finally as for 2.0 petrol vs 1.9 turbo-diesel, it's a matter of taste. I have a 2.0 petrol because I loved the 2.0 petrol in my previous Alfa (a 147) and didn't really feel the need to change. It's a smooth, deceptively powerful engine, and I love it. The 1.9JTD has more torque, being a diesel, but in its unadulterated form it's out-performed by the petrol, which is why a lot of people on here get it modified (chipped). However, there are those that swear it's the best engine for the model, so drive both and make your mind up.