To me the engine is a part of what gives a certain car its character. A car with an Arese V6 has a certain something.
Sorry, but I have no experience with engine transplants. However, it makes much more sense to me that the Arese 3.2 would be your choice of the two, because it will definitely fit into the car. The newer 3.2 would surely take a lot of work, and possible not fit at all; such things as engine mounts, gearbox, driveshafts, cooling systems, electrical integration, etc, etc. You could probably buy a GTA for the cost of the engine and fitment!
So, focus on the Arese. But also be mindful of: cooling systems, driveshafts, front brakes/hubs, gearbox, ECU/looms, etc. Still wouldn't be a quick changeover, and not 'just the engine' that you'd be wanting to change. So a complete 'front cut' of a GTA is what you'd want to buy I think. Maybe speak to pud237 about it, cos I believe he upgraded his 2.5 to the 3.2.
As per my original post, the "certain something" about the Arese is surely only how it looks. Not saying this isn't a valid point, but performance wise, I cannot see how it's better than the new engine.