The MSI version of the 680 is superior it has a far superior cooling system, its also faster then stock.
However that being said I don't think the price warrants the cost. I feel you are better off with the EVGA card for the following reasons. You don't lose anything in terms of performance or anything you could measure. You also get a stronger customer support experience with EVGA they are a more direct NVIDIA supplier so you will have a faster turn around time with RMA's. The only con I can think of is the cooling system on the 680 by EVGA is inferior to any aftermarket cooler out there by ASUS, GIGABYTE, and MSI.
IF you were looking for a superior cooling solution for a cheaper price I would look at possibly the 680 TOP from ASUS.http://www.newegg.com/Product/Product.aspx?Item=N82E16814121634