The complete lack of marketing has to be No. 1. I don't recall seeing an ad anywhere.
I originally thought that the Baldur's Gate successor genre was running out of steam since DAO started it, but Pathfinder Kingmaker did really well, so I doubt that is it.
The game is so badly optimized that I think word of mouth turned a lot of people off. I still runs like garbage today, and has been abandoned by the devs. The load times were ridiculous. I pretty much try to avoid Queen's Berth at every opportunity, because I don't want to sit through a five minute loading screen every time I exit a building. The vast quantity of loading screens in general. By all accounts, the console port is even worse.
Even if it had sold better, the game was over-budgeted. I don't know how much they paid Mercer and friends to hang out, but it was too much. Not sure why they threw this much money at a niche product, and expected to make a profit. For all they spent, the game doesn't work nearly as good as the budget would indicate.
That said, I love the game despite the flaws. I prefer it to DOS2, and liked it better than Kingmaker, at least until Kingmaker got patched up.