the biggest issue is warranty and warranty service. what vendor will live up to there life time warranty without people jumping through hoops. also how fast can you get the ram done and will the cross ship.
I would say the build quality. Not all manufacturers use the same quality parts whan building their GPUs. It would be safest to purchase "trusted" brand GPU to rether than experimenting with a cheaper one to save a couple of bucks.
My personal opinion is that if you are new at building your best bet would be to find a GPU from the manufacturer of your mobo if possible. Otherwise just read up as much as you can find on the GPU you are interested in so thet you don't have any unexpected surprises later.