Yeah, there's probably a lot of unjustified outrage over this matter, but Gearbox's Randy Pitchord has been no stranger to controversy, he championed Duke Nukem Forever and nearly pulled an Eidos with that game. Aliens: Colonial Marines is a little more dramatic.
Nobody expected Duke Nukem Forever even half as good, because at that point, the game was simply a joke to the entire industry. Gearbox made a lot of noise about that game, but really their involvement was minimal, since they had 3 smaller devs doing the grunt work, they didn't bother with cleaning up most of the issues, they went in with the average programmer mentality which is: release now, fix later.
Aliens: Colonial Marines on the other hand, wasn't the case, Gearbox seemed to take advantage of SEGA's leniency for other purposes, especially with Borderlands 2.
When a game that took 6 years to make is worse than a game that took about 18 months to produce, people are going to start asking questions...