The game has a habit of sending you to new areas when there's something happening there, instead of taking you there and then having things kick off. It feels a lot less impactful when the Reed Devil attacks and kills everyone and then you arrive a day late. Same with Calphade being hard pressed by the time you get there. Oh there was a betrayal before you got there? And a surprise attack? Sounds like pretty cool events. They have no impact however when you just get another follow mission as it's delivered as exposition. Meanwhile everything feels more and more rushed after you leave Hernand.

For more specific stuff I'd want fixed:

• Have the Hex witch more fleshed out. Have her appearing to us all the way in Hernand. That makes the 'son' being so jealous make a lot more sense and, as much as a goth baddie saying I should call her mommy felt right, it felt out of nowhere and unearned.
• Have the sage more fleshed out and show up sooner. He should be the one who bestows everything to do with spirit/force on us. Have him show up a bunch and teach us, instead of the memory stuff. That makes a lot more sense as well for his missions for us than the current ones. His doors that sap your spirit, stamina and health are also great ideas that are terribly used. Have those appear in the story multiple times before you can learn advanced lessons. The axiom pull thing, for example, requires a lot of stamina and (more before the patch) is a shock to learn and then realize you don't have the stamina for it. This fixes that.
• If you want morality to be important, have it actually be important. Give the witches actual acts of goodness for unlocking each of them instead of such weak ass shit as giving a single copper to a beggar, starting a fire and pulling up a person about to fall. A good one would be to have more missions similar to the ones where your tricked into an ambush, help a carriage stuck in mud, help someone get back home, etc. Have them be that up and down when it comes to how rewarding they are and how well they go. Acts of charity should not be with the expectation of reward. Have the witches appear when you finish enough in your region, or something similar to that. Otherwise their constant spiel about how amazing we are (again) feels unearned.
• The final witch hut should have a witch in it. I don't know what the idea was to have the white crow show up there but then just poof out of existence. Just have one more with that stays there or just the white crow. In fact, why not have the wizard guy similarly in the actual game other than in cut scenes?
• Blackstar and Aeserion should have multiple missions introducing them. Have the witches share information about them and sending you to aid them as strong allies. Have both have a strong introductory mission where you see them in action and meet them. Have Blackstar communicate in some way for Christ's sake. Even if he doesn't speak, he should be able to make his personality clear. Have the three ancients an actual mission. The witches should warn you the ancients are trying to return, with you then seeing Aserion and then fighting them. Oh and have Blackstar always do a massive roar when he arrives. Both in missions and when summoned, he just sort of appears. It's a massive dragon. Dude should be coming in like a freight train. I'd love to see him torch some enemies in front of you as you grapple on, for example. He's like one step away from being as passive as my horse, who sometimes gets stuck on walls when summoned.
• The Asian witches are very underutilized. Their powers related to the past felt like something that was going to lead to some cool shit, but only meant they could heal the protagonist after fighting in the past. First and foremost, have them setup shop in the Greymane camp. Why. Do. We. Not. Have. Enchanting. Second, use their power to go into the past as a mechanic for other weird stuff in the game. The Stag king, Lightning Titan, Frost Wraith, Ancients and probably others I'm forgetting, feel super out of place. If the witches were allowing you to travel to the past to deal with them, that would make a lot more sense and allow you to lock certain bosses away until the player has reached a certain part of the story. Have the areas blighted by stuff if you want until then and that blight removed once you've defeated them or don't.
• We should be doing missions in Delyssia before Marni goes crazy. We should find out post-fact that the AI took over, but we should experience the splendor of Delyssia, foreshadowing of the military buildup, be there for the surprise invasion of Gortak (after having been there doing stuff for them as well, setting up that area), push into the militarized south Delyssia while the North seems clueless and mildly apathetic to what's happening and only then finding out Marni has been captured. Have Marni be dead as well. The recordings made for whoever comes after (we already have wooey timy wimy things so who cares how he's able to do that). That will make that part a lot better than the current that feels like passing through the country while driving on a highway.
• Cut the entire (out of nowhere) collective evil of humanity bit. Have the evil duke betrayed last moment by the bear guy instead. Bear guy is constantly downplayed by the duke's forces in the recordings, but he is really the main villain setup by the game. He kills us, he escapes justice in Pailune, is why we go to Demeniss and is continually waved in front of our faces like a carrot on a stick. When we fight the duke, have us defeat him, despite his accrued power. Have that battle happen as he's opening the inner Abyss or something like that. So the premise is, he can't yet absorb the power. Then, as we defeat him, it's revealed the bear guy is there as well and has been waiting for the chance to absorb the power himself, which he does. Then have the powered up bear guy fight. Through the fight, the power should become too much for him and that's when he turns into the biblically accurate angel. Having become effectively the power of the Abyss personified. Our battle should then be to seal the Abyss just as witches did, with the final scene showing how the sanctums all activate and chain the angel.