A couple of changes to the Emmy rules for this year could affect FG.
First, the plan is for there to be only six nominees in the Comedy Series category - the rule about allowing a seventh if it is within 2% of the votes of the sixth nominee in the nominating ballots has been rewritten to apply only to categories where there are normally only five nominees. (There is a chance of seven nominees, but only if there is a tie for sixth - and even at that, going by a strict reading of the rules, it is more likely that they would have only five nominees instead of seven.) With Glee being added to the mix, it's going to be harder for FG to get a nomination in this category, and since the writers and directors don't get any awards if the show wins (unlike in the Animated Program category), and probably won't get any nominations in the writing and directing categories, I wouldn't be surprised if FG goes back to the animation category this year.
Second, there is no more separate category for animated shows that are one hour or longer - all animated shows compete against each other for a single Emmy. (Actually, there is a second category, but it is for shows that are 15 minutes or less - for example, most episodes of Robot Chicken.)