I have kids, and let me tell you, Emirates is far more established and all. They have a much stronger reputation in this part of the world. They also have a established links with companies and schools and the like.
If your kids end up going to JESS school lets say, Emirates will pay your debenture for your child. FD on the other hand, you're on your own.
Go anywhere for discounts (eg FedEx, Car Rental places etc) and they have agreements in place for EK, but not FD. These aren't make or break points, but just a few 'extras' to think about in the overall scheme of things.
I know these are small (some may say petty) things, but over a period of 10 years, it all adds up.