Take two doesnt care about A:CM at all, but Gearbox does. Their name is attached to the front of the box and Randy Pitchford was leading the PR for the game, even though it appears they contracted a lot of the work out to other studios, it is a huge stain on their reputation.
The last 4 major releases for Gearbox were Borderlands 1, Duke Nukem Forever, Borderlands 2, and Aliens: Colonial Marines. While Borderlands 1/2 were money makers for Gearbox, Duke Nukem and A:CM were turds. Unless Gearbox wants to be stuck making Borderland games forever, they have to build up good will with the public and more importantly with publishers. Take 2 published DNF, so they also took a hit, but I read somewhere they didnt lose money on the game although they probably didnt make much either.
They are ok with Take Two for the most part, but Im sure they will be pushing for more Borderlands and less likely to allow them to work on a new ip. If they can repair their reputation, hopefully they can find a publisher that will allow them to work on a new ip for next gen systems. They still have a good relationship with Ubisoft working on the Brothers in Arms series, and a new game in the series is due out this year.
While Im looking forward to a next gen Borderlands game, I want to see what they can do with a new ip and maybe a new genre when they have control of development from the start. Duke Nukem and A:CM were a hot mess when Gearbox took over development, and it is hard to tell how much blames lies with them. Its possible the games were beyond saving, but if a publisher was willing to give them the money to try, I dont blame them for taking the money and trying.