First off, due to me breaking NDA, I can't provide any proof that I'm not just talking out of my ass. But I figure you'd be interested in hearing what I have to say regardless. I've been on the project for around a year and a half, so some of the following are things I've heard from more senior guys.
Pecan (the internal codename for ACM) has a pretty long history. SEGA, GBX and 20th Century FOX came to an agreement to produce an Aliens game around 6 years ago, after which SEGA almost immediately announced it, long before Pecan had even started production. The game has been in active development in the past, only to be shelved in favor of another project (Borderlands, Duke, etc), and each time it was resumed it would undergo a major content overhaul.
SEGA, naturally, wasn't super pleased about the delays, but GBX got away with it for a long time and the contract between SEGA and GBX kept getting augmented to push the projected release further and further back. The last time it was resumed, GBX outsourced a good portion of the game to outside companies. Initially, the plan was for TimeGate to take the majority of campaign, GBX would take MP, Demiurge and Nerve would handle DLC and various other focused tasks. This decision was made mostly so that most of the developers at GBX could continue working on Borderlands 2, while a small group of LDs, coders and designers dealt with Pecan.
Somehow the schedules for Pecan and Borderlands 2 managed to line up and GBX realized that there was no fucking way they could cert and ship two titles at the same time. Additionally, campaign (which was being developed by TimeGate) was extremely far behind, even as Pecan's Beta deadline got closer and closer. In April or May (can't remember which), Pecan was supposed to hit beta, but GBX instead came to an agreement with SEGA that they would push the release date back one more time, buying GBX around 9 mos extension.
About 5 of those 9 months went to shipping BL2. In that time, TimeGate managed to scrap together 85% of the campaign, but once Borderlands 2 shipped and GBX turned its attention to Pecan, it became pretty apparent that what had been made was in a pretty horrid state. Campaign didn't make much sense, the boss fights weren't implemented, PS3 was way over memory, etcetcetc. GBX was pretty unhappy with TG's work, and some of Campaign maps were just completely redesigned from scratch. There were some last minute feature requests, most notably female marines, and the general consensus among GBX devs was that there was no way this game was going to be good by ship. There just wasn't enough time.
Considering that SEGA was pretty close to taking legal action against GBX, asking for an extension wasn't an option, and so Pecan crash-landed through certification and shipping. Features that were planned were oversimplified, or shoved in (a good example of this are challenges, which are in an incredibly illogical order). Issues that didn't cause 100% blockers were generally ignored, with the exception of absolutely horrible problems. This isn't because GBX didn't care, mind you. At a certain point, they couldn't risk changing ANYTHING that might cause them to fail certification or break some other system. And so, the product you see is what you get.
Beyond gameplay, the story has been raised as an issue several times. I can't really comment without feeling bad beyond saying that the script was approved by 20th Century FOX, and that the rush to throw a playable product together came at the cost of the story. Campaign does a pretty bad job of explaining a lot of the questions raised at the start of the game, and so hopefully there will be DLC to flesh that out a bit better.
