Sure thing. One thing before I start, I'm not counting SoD as part of the canon. This is largely due to it being created well after the fact by a third party, making the narrative basically fan-fiction to me. Like, I'm not looking down on it for being third party, but the story in the core games is rough enough as is, we don't need SoD stirring the pot. Besides, James Ohlen had nothing to do with SoD, right?
The short version is that it seems to me there were a lot of choices that solved a problem in the moment, but the further reaching effects were not considered. I think a lot of the answers that came after the fact were due to people asking questions, but the answers just lead to more questions. None of the story feels like it organically emerged, but more that a creative wall was hit, and something was needed to get over that particular obstacle in that moment.
The first game was pretty tight. The whole god-blooded storyline was a tad over-the-top for me based on my own experiences with D&D but a) everybody has a different experience with this game and something so epic is not inappropriate at all, b) this is an essentially single-player video game so that is going to have an impact on narrative emphasis, and most importantly, c) from a literary perspective, it does work, for the most part. I'm good with the first game. I wouldn't run that at the table, but in a video game it's good stuff. All in all, it's a 4/5 game for me.
Baldur's Gate is basically D&D Highlander. Except, 'there can be only one' is less the ultimate prize, but the resurrection of Bhaal. I'm ok with this. I had a friend who was well versed in ancient Greek literature and basically said that the Greeks have already told every story and we just keep rebooting it. As long as we do an interesting job of it and the craft is good, it's all cool to me. But, there's so many questions that can pop up with Baldur's Gate timeline. Alaundo's prophecies were more than a millenium before the Time of Troubles. What people were doing about Bhaalspawn before 'The Gathering' is a mystery. The whole thing about the cult where Sarevok, Imoen, and GW were found also raises a lot of questions. How did the cult find and gather all these kids and everyone else was doing nothing about it? How did the meticuluous Harpers miss the seven-year-old (Sarevok) in the mix. I think it was written off as the 'chaos' of the raid, but the Harpers basically wiped out the cultists. Chaos is over with a bunch of kids sitting around. It all just seems like a handwave.
Then we have the second game, which basically hinges not just on Imoen, but her character having a massive paradigm shift. I mean, she was originally never supposed to leave Candlekeep, but then they grow her into an NPC. I'm good with that. It's a good move. She's a plucky, light-hearted, precocious rogue which not only balances out the gravity of GW's situation, but also provides you with a skill monkey that is generally needed in a D&D game. Then they turn her into something completely different in the second game. She happens to become a mage somewhere during your adventures in the first game (I believe SoD retcons this a little, but I'm ignoring that) which really feels like it wasn't true to the character, but done just to contrive a plot hook to get characters on track in the second game. I can also criticize this on a gameplay level. That is, it is now a pain in the ass to play the implied canon party in the first game with an Imoen dual at level 6 or 7 (it's hard to say which is accurate since they borked her stats in the second game). I mean, it was a thing that happened and was written. You can't argue that, but why this choice?
And why Irenicus? His story isn't bad, but it is also only tangentally germane to GW. I think there is a strong narrative to present there, but he reeks of side quest. If anything, I would have flipped the narrative emphasis of ToB and SoA. ToB was the culmination of GW's story and that should have been more than an expansion. That should have been the second game. At the end of it, GW is presumably the last Bhaalspawn* after ToB (except for Viekang, wherever he pissed off to), making him Irenicus' last hope (at least in the wizard's mind). His story didn't need a full game, but would have made a more solid expansion. Keep in mind, prior to the end of ToB, Irenicus had many more options, and probably easier targets than the bhaalspawn that just saved the entire Sword Coast. If you flipped SoA and ToB, you would just have GW, Imoen, and Viekang as the last Bhaalspawn (and Viekang would have made a great plot device as a failed initial experiment of Irenicus). You could still kidnap Imoen, you still get the Yoshimo story, you don't even need the narratively absurd cowled wizards or Imoen's uncharacteristic and contrived dual class. You just have a shorter investigative journey to track down your best friend and save her. Thus completes the saga (until BG3, of course). This also would have worked well because most people would also probably keep Yoshimo around to have a thief (easy direct replacement), making his betrayal even more impactful (I've always tried to keep him in BG2 for this reason).
This would have been a much stronger narrative. It could have avoided the absurdity of the cowled wizards. For example, I go to spellhold for casting Friends, but a cleric can gate a demon into Waukeen's Promenade and they don't care? The narrative could have been constructed differently so you don't have the mismatch between needing to rush and save Imoen versus wanting to sidequest a bunch in chapter 2 to gather loot and swag (you basically have enough gold to go get her by the end of Nalia's quest). I just think it would have all flowed a lot better and made for a stronger game.
I mean, there are so many different things you can nitpick on with the writing on this one, but the more I think about it, the more I think almost all of it could have been solved with flipping SoA and ToB. So yeah, what was what happened what was chosen instead?
*The metaphysical implications of Imoen and Sarevok dying as Bhaalspawn and then coming back is a whole other conversation and pulling at this thread could unravel the entire story, quite frankly.