"This is what they worry about"
I doubt that adding this to the game is some how a detriment to other features, as if this was their number 1 priority when they began planning for madden 16. I do think they should have an option to skip or quit out of this intro however. I don't mind playing but I know some other people would like to get right into the game.
As for the two teams I saw someone say Colt and Packers and that sounds like a good choice, though I personally don't see the Colts as a favorite to make the superbowl. I could see the Patriots being a team but they might want to avoid them do to the "deflategate" scandal. Seahawks could even be there too but they might want to do a different team this year. No matter who it is I'm looking forward to this intro. It was fun booting up the game last year and immediately being immersed in a big game situation.