I just finished the game myself. I thought it was pretty good, but yeah I can definitely see some of the criticisms people are making.
The game definitely does not give you enough time to get INVESTED in the gods and the setting to have the big reveal that they are "fake" have much meaning. Which is a shame, because they seem very interesting. Which also makes it sort of disappointing that their quests seemed so short and rushed.
I think the third act could have been made much stronger by focusing more on the gods. This is a morally ambiguous, capricious, self-serving pagan pantheon. I did like some of the touches in the quests (particularly Berath's, where his followers were not particularly impressed by you being his messenger, and not particularly impressed with the judgment of their god, or Rymrgrands, where his 'followers' were actively trying to defy him)
Really, a big recurring message of the game is how the people of the world "worship" gods in ways that we're unfamiliar with. Eothas and Hylea are probably the closest to what we consider as sort of "traditional" gods, in the idea that people pray to them expecting boons, comfort and benefits. (Though even they are not completely familiar, what with Eothas actively leading a war, and Eder, one of his worshippers, going to war against him) But all the other gods are worshiped in ways that seem very unfamiliar to us (Durance constantly calling Magran a "whore", loving and hating her at the same time, etc.) In fact, almost every time you meet a group of people who are 'worshiping' a god, what the worshipers are trying to do often completely contradicts what the god wants. The only exceptions to this that I can think of, in fact, are Thaos, and the Skaen cult. And maybe the fangs, with Galawain.
But anyway, yeah, the third act could have been made stronger. Maybe instead of introducing a "Oh no, have to catch Thaos before he hands the souls over to Woedica" element so early on, you could have the party make it to the city before he actually even makes it there. You try to win the favor of the gods to help intercepting him, but they are unwilling, until Thaos pulls off some really crazy **** to make it through the city. Give some more meat to the plot, give you more of a reason to linger. Have the final fight actually make SENSE (Thaos made it to the machine much, much earlier than you did - why didn't he just hand off the souls to Woedica before you even got there?)
And yeah, the elven lady at the end was just...pointless. Should have built her up more. Could have made her a bigger part of the Watcher's "madness" throughout the game. Might have actually felt the impact when you finally meet her, then.
And yes, the final dungeon was also underwhelming. You didn't need to throw tons of enemies at me or anything, but....this is the pinnacle of achievement of an ancient, super-advanced culture. The site where they killed themselves to forge the gods. I don't know, maybe there could have been some symbolic puzzles, some flavor, meat that sort of gave you an idea of the alien nature of the Engwithians.
And yes, it did sort of feel like, towards the end, the game shifted in tone from "Look at this interesting pantheon of morally ambiguous gods and the strange ways they are worshiped" To "Gods are a lie! Religion bad!" which is just NOT a novel message anymore. In fact, it's awfully boring, predictable and grating, and that's coming from an atheist. I would have built up the threat of Woedica more, (she basically sounds like the goddess of totalitarianism), made the big reveal something more personal in nature (like, I dunno, maybe Thaos is decoupled not just from the wheel, but from time too, and the 'connection' between you two is that you are actually one of his incarnations, and he's basically committing suicide?) and save the big reveal of "gods aren't real" of this game for a future game, when we've had more chance to become attached, and accept the gods as a given of the setting.
I liked a lot about this game - for example, Eder's companion quest, I liked how the ending was basically just that he had to live, never knowing why his brother did what he did - but I can't help but feel that they definitely stumbled in the third act.