This is an interesting question. To me, in season 1, the spotlight actually seemed to be more on the the pros than the rookies (although I will admit I didn't watch episodes where they were running obstacle courses and selling programs and all that nonsense). So in season 1, I didn't feel like I really knew who most of these rookies were, the only ones who really stood out to me in any way was skip (because he was turned into a joke), and bryan because of his feud with the miz and cole. No one seemed to really shine in the ring, and even by the finale, I still didn't really know who barrett was or why he was still around.
Now that nexus is running around, you still don't really know much about these guys, they are just mindless interchangeable drones, outside of their barrett mouthpiece.
On the other hand, I feel like season 2 of nxt has really taken the spotlight away from the pros (in fact, the presence of the pros around the rookies seems pretty inconsequential) and we have a better idea of who these guys are, individually. So for that reason I think it's easier to think that season 2 would make a better nexus because they seem more like a group of unique individuals than a mob full of unknowns and unimportant folks.
Also, and this may just be based on what I've seen of each, it seems that in general, the folks from season 2 are better in the ring than season 1.