I think Mueller and Little are two of the most similar players from the 2006 draft. Mueller is significantly bigger, but neither is a real physical force. Both are responsible defensively and reliable offensively, with noted intangibles. Little is probably more proven, but I'd say Mueller has a higher top-end. Bryan Little is going into a (most likely) better situation where he may one day center a line with Ilya Kovalchuk and Marian Hossa on his wings. If that's the case, it's tough to argue Mueller will outscore him, and in the same situation, it's likely Mueller would not score as much. At the same time, I feel that Mueller is much better suited to the situation he's going into in Phoenix, so it's one of those "both teams win" situations.
Now, since I've spent a whole paragraph dodging the simple question you asked, I'll conclude with "While he may not score as much, I think Peter Mueller will be the better player overall."