Every card, for any given series, is going to USUALLY, barring any monumental problems with a specific card like we've seen recently in reviews of the THICC cards, perform within about five percent of any other card within the series so long as cooling isn't an issue. For 99% of cards, as long as there is sufficient case airflow, it isn't.
So, that being said, product support becomes pretty much the biggest factor and selling point aside from whether or not the card will even fit your case, and in that area, I think if we are going to exclude EVGA, then MSI is going to beat out Gigabyte in the area of support after the sale. That is not to say that Gigabyte has "poor" support, but I've found their product support to not be as friendly or fast as MSI, and MSI seems to have a better global presence as far as I can tell as well. There are some regions where Gigabyte seems not to be in that market at all, whereas MSI is pretty much worldwide.