We had little to no time to redo anims, redo character models, redo locations from previous iterations, so we did what we could with what he had, and it made sense to us for the time frame (even when the time frame kept changing, we had no clue the release date would be what it became, and we didn't work toward that release date).
This, I think, speaks a lot about why Alpha Protocol came out as it is.
EDIT : I wonder WHY they had to scrap that first iteration in the first place though.