I have similar feelings. I went through a period of feeling a little down, partly because I'd spent so long anticipating this game that it could never live up to the hopes I'd built in my head and partly because the story just didn't fulfill everything it previously promised.
For the Leliana thing, yes. I really think that in that case, there should have been an alternate spymaster. It would make sense if they were less quick at war table missions and had fewer contacts, as well as none of the cutscenes and focus on characterization.
Lol. They could have made them a tranquil mage. Imagine listening to that creepy monotone every time you set your spymaster on a task. What could be more fitting in a world state where someone was killed over the corruption of a sacred religious artifact?
And for Varric, they definitely should have had something happen. I think he have probably become consumed by it, maybe with a way for the Inquisitor to help him if they did things just so (finished his missions and "analyzed" the red lyrium, maybe arcane research perk). The whole treated of red lyrium in DAI drives me a little bonkers. It's played as very dangerous in DA2, and then it DAI its...informed to be dangerous, and yet we still treat it as handy little thing to carry around and stuff into our weapons?
I agree, Inquisition often seemed to play things a little too safe, rather than take chances like DA2 did with the status quo, or how Origins gave us quite varying outcomes? It's not that DAI let me down per se, but it did seem to wrap things up way too neatly with a nice bow, when some things should have perhaps remained unsolved and left hanging, like perhaps the Orlesian Civil War?
I'd have preferred just a better explanation for Leliana than "I got better". While it might have been a rip off of Wynne's storyline, having Leliana be resurrected by a Spirit of Faith would have been been a far easier handwave and fit within the lore established? There were numerous entities in the Temple that were most likely Spirits (since they can get inside your head), so any one of them could have saved her? Could even have been the Guardian, himself? You are forced to "kill" him if you desicrate the Ashes, so if he merged with her, it would have saved them both?
The Red Lyrium stuff irked me as well, in my first playthrough I was paranoid of even having any weapon with a Corrupting Rune enchantment being anywhere near my character, for fear that it could lead to some kind of problem later on?
In DA2, a small sliver of the stuff was enough to cause all manner of spooky do in Bartrand's house, yet in Emprise du Lion we have soldiers next to huge mountains of the stuff, with no consequences? It's danger level became just an informed attribute, rather than something that was actively a danger to anyone? Having it cause even a mild status effect that saps health etc, whenever you're near to it would have been enough?
"In Hushed Whispers" would have been even darker if our infected companions turned on us and we were forced to kill them? It bugged me that they were still so rational and themselves, despite having been exposed to it on a daily basis for over a year? Having them paranoid that we were a demon impersonating the Inquisitor and attempting to kill us, would have at least been understandable, since they'd spent the better part of that year believing we were supposedly "dead" after Alexius blew us up?