2D might not look pretty, but it's by far the best tool for the job at the moment.
As has already been pointed out, the best 3D engines are not capable of presenting a realistic game at present so it would be stupid to change from an engine, that whilst not perfect, is currently the best around at presenting a realistic game of football.
Also, as Katarian pointed out, for a tactical game, the top down engine allows us far greater insight into how our tactics are working. A move to 3D could restrict our view of the pitch, making tactical decisions much more diffivult to make.