Huh, I laughed at @Make a contract with KP's joke. David Lynch is famous for just saying no every time someone asks him to elaborate on the meaning of one of his films. Dune aside, but Dune was directed by Alan Smithee. It is also an answer of a sort, more than it would initially seem.
What made Pillars of Eternity so unremarkable, or perhaps boring, for me, is not any one thing, it is a combination of many little things. As far as the writing goes, that is a little more difficult to quantify as I have yet to figure out what I really consider 'interesting' or 'good' beyond a few examples I can point to (one of them would be Neon Genesis Evangelion, which manages to be geniuinely interesting sci-fi, a deconstructionist examination of an 80ies sci-fi staple and a deep examination of depression, need for validation, pressure and loneliness - the director of the series expressed his own personal experiences through the characters, and it shows). I can point to a larger number of things that generally qualify as being well written but do nothing for me: Icewind Dale, Pillars of Eternity, and The Great Gatsby, which already caused groaning in the book thread, but I have to bring it up again, because it has the exact same issue. Reading it was unengaging. It took me longer to go through it's 200-something pages than reading a doorstopper novel generally considered to not be worthwhile by literature experts.
Now, the Fitzgerald novel at least I can point to and say that neither the time period nor the social circles it is about are of any interest to me, so that could explain my experience, but ruminations on the existence of souls and the nature of gods, an ancient, lost civilisation and a conspiracy to hide it all? Count me in. There were a handful of interesting moments in Pillars of Eternity. The parts of the main story in Defiance Bay and particularily the visit to the Sanatorium stand out, and when Thaos showed up to conclude the second act, at this point I thought the game would finally rise to its promise, at least in terms of storytelling - and it went back to being what it was before almost immediately.
The combat gameplay is a factor as well, as was my experience with the first few patches. I may have mentioned it before, but my first - and only - character that I played Pillars of Eternity with was a Cipher with a blunderbuss. The first couple of patches made my game experience worse in the name of 'balance' - because rogues arguably sucked when the game launched, my Cipher's ability to bypass the unfun combat were tuned down, instead of rogues being made stronger. Why? The only reasonable answer I have is that the designers of the game actually believed their combat to be fun, and for it to be fun, it needed a serious trimming down in options to bypass it more quickly.
The idea is preposterous to me, because combat in Pillars is a slog. It feels unresponsive even though it gives much better feedback than other real time with pause isometric games, and the pacing feels off. The graze mechanic, put into the game to give the players a minor success instead of dice rolled miss streaks, like they were all too common in Baldur's Gate or Icewind Dale at the lower levels, made the combat feel even worse than better, and again, that is by far and large, based on a feeling. The entire time I played Pillars, I thought the game would play better as a turn based game.
Now, if someone actually enjoys the combat of the game, and I am certain there are people who do, then it becomes a much better experience.
There are a handful of other game elements that came from the success of the Kickstarter campaign. The stronghold mechanics feel like they were tacked on later, and Twin Elms is a break in pace at a point where the game shold move towards its conclusion. Both came from stretch goals. A number of other Kickstarters with runaway success had the same issue.