I don't like this idea.
A 11-5 team isnt neccessarily better than a 9-7 team. Look at the opponents in the AFC we had this year and what teams the Bucs had to play. Compare MIA, BUF, NYJ, NE with HOU, JAC, IND and TEN and you cant really say that the Giants deserve homefield over the Bucs here. Giants are 3-1, Bucs are 1-3 in interconference games. Of course you can say, thats because they are better, but I dont think thats the whole story. The same argument counts when you compare the strength of divisions.
I dont see the need to change the system. If the Giants want homefield they have to win the division, thats all, every team starts at 0-0.