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.