It's an interesting thought, but there are too many logistical problems in my opinion.
World Cup games only come out every 4 years, and a regular FIFA comes out every year, you can play a lot more than 4 years in career mode- thus requiring multiple transitions, the NCAA>NFL transition is a permanent one- whereas players go from the World Cup back to clubs, and the games would need a way of knowing if your player is selected to the squad, as well as who else is selected to the squad.