The way I understood it, and it may not be true for everyone else, but the problem was not that they brought in Jack, but rather that they killed John at the end, which forced you to do free roam with Jack.
Personally, I liked the ending because it was new and different, and I liked how they set Jack to get revenge, but it was a mistake to not bring back a way to play as John, except for replaying the missions. I think when you spend an entire game building up a character and his story, and then replace him at the end, it's hard for people to accept the new guy no matter who he is.