I think there might have been exhaustion with Pillars 1 and no desire to play more of it in a sequel, and it's also possible that some players may have felt like they had to play the first one before the sequel... I really doubt it had anything to do with the sequel's quality, I think the issue might have been people's nostalgia for "Baldur's GatE" had played out during the first campaign.
Could also argue that Fig didn't market Deadfire well and Fig doesn't have the same attention-grabbing aspects that Kickstarter does, but I can understand with the Obsidian owners being on Fig's board, it was important that they use Fig, even for all its fault and how it might hurt the sales of Deadfire - which seems counterproductive. I also feel bad for the Fig investors in the product, they got screwed as well, but that's the risk you take.
Have to confess, I thought Pillars 1 was okay, but I definitely thought the story and characters in the sequel were worse... but that didn't affect my purchase, as I didn't know how the story and characters would be when buying it.
I know there was mention of a lot of bugs in Pillars 2's release, so that could have slowed sales as well. It could have done with some more delays for quality, but it looks like they fixed them all (at least the PC version, the console versions still seem kind of... eh).