Before the start of the season, I think most would agree that Wiggins will easily do better than Nibali. However the results of Tirreno-Adriatico and Catalunya made too many people believe that the tide has changed and the results now favour Nibali.
Personally, I think that we haven't seen enough of the two this season to call it one way or the other. Winning Tirreno-Adriatico was a good result, but it was a result of one brilliant stage masking indifferent results in the two prior stage. While Nibali did great on Stage 3 to finish in front of everyone but Froome and Santambrogia, it wouldn't be too hard to imagine that if it were Wiggins instead of Froome sitting behind Uran, Wiggins would have made the bridge like Froome did before sitting on Nibali's wheel the rest of the way. On Stage 4, Nibali cracked behind all his rivals, showing that he can be inconsistent too.
Volta a Catalunya stages 3 and 4 I think shows what Wiggins can do with and without his train. With his train, he was able to match the likes of Rodriguez and Valverde - riders that are arguably at least as good as Nibali at climbing. Without his train, Wiggins cracked badly on stage 4. The good news for Wiggins is that the circumstances that led to his train being burnt by the final climb is unlikely to happen in the Giro.
All in all, I think Wiggins still has a slight edge over Nibali, too small to really call it for Wiggins with any significant amount of certainty, because Nibali can still beat him if a combination of some of the following things happen:
1. Wiggin's TT form for this season is still a question mark as we haven't seen him TT at all. Could he be completely out of form? Even out of form, it is still hard to see him losing to Nibali in the TTs.
2. Can Nibali make several repeats of Tirreno-Adriatico stage 5? I don't think there are enough stages like that in the Giro to make a significant difference.
3. Can Wiggins be isolated from his train? Possible, but I think it is harder to achieve this in a Grand Tour than in a normal stage race, with the extra rider and the vastly reduced necessity to chase down breaks.
4. Can Nibali put in a few explosive bursts at the end of a climb to put time into Wiggins? It's possible but IMO, results show that he isn't that kind of climber.