I was thinking about this earlier today to pass the time, what could have been different/what I would have done.
How could they have brought Diablo back without using the Black Soulstone route? If the Prince Aidan/Dark Wanderer x Adria angle is retained, I thought of this cinematic from E3 1998 and how he leaves a chunk of the soulstone behind. If Diablo/Aidan had left part of his soulstone with Adria (or just let it drop in some random town I guess) that could be used to explain the whole 'How can he be back if we smashed it on the Hellforge?' bit a little better than 'Adria marked all their souls for the Black Soulstone, suck to be you.' Mephisto would be the only one 'KIA' since his soulstone did get smashed in full, but I would probably have Belial/Azmodan find a way to steal his essence to further their goals/go towards becoming the Prime.
Tyrael would definitely not have made himself mortal. It's just silly, and I don't think there is any example of that ever occurring throughout the Eternal Conflict. If he has to fall from grace, I would make it similar to the Dark Exile where he willingly banished himself in spirit form to Sanctuary, where he then could possess a willing host. At the end of the game the Crystal Arch could still offer him Wisdom instead of Justice, but he wouldn't be an idiot and think Justice was 'met' by disintegrating Diablo and just having him trapped in the Black Soulstone. (Auriel wouldn't think that 'all evil' was vanquished by defeating Diablo then, either)
Deckard Cain would either not die, or do so in a way that didn't upset fans nearly as much. There's all these prophecies about the final battle between demons and man, the end of all things, the end of days (Besides a reference in the promo materiel for RoS, was this even mentioned at all in Act V? It's like they just completely forgot about all of this in-game), and they kill off the one guy that had dedicated his life to them in the first Act. According to the Behind the Scenes, Leah was supposed to become 'the new Cain' for us. Perhaps if Deckard was willing to be Tyrael's host, that makes him a target for Belial/Azmodan and he is killed for that reason, by a major Evil and not some dragonfly witch. Leah would also actually believe in the 'stories' Deckard was trying to teach her, and not be trying to burn the Book of Cain after he died, and actually become that 'new Cain' that they wanted her to be until Adria's betrayal.
The Belial 'deception' needs a lot of work. Make there be an 'evil' vizier that gets all the blame or something, making everyone think he is that guy while secretly being the innocent character all along. Have him flee into his Realm of Lies where it is said nothing is as it seems, and what first appears to be a paradise of beautiful growth and pleasure is revealed to be full of torturous traps, illusions, mazes, a realm where a maggot-ridden piece of food may be the most nutritious around, and every time an unlucky soul falls into a trap, Belial's laughter would echo.
The original Horadrim had to dismantle Zoltun Kulle's body and magically imprison the pieces to keep him 'dead.' We did nothing of the sort. This bit is kind of messy, I think at least having Adria be with us and she being the one to initiate the attack might make more sense. She attacks him to stop him from revealing what she had done to his work, Leah goes to save her mom, we attack to save Leah. He would, and maybe will, come back later on now that Malthael has proven to The Nephalem that the angels aren't really on our side and the only way out is to rise against both order and chaos.
Not sure what to do with Black Soulstone. Was kind of lame that they had Tyrael telling us we had to smash it, then it ends up being 'Oh, uh, we didn't know if smashing it would be okay' in RoS. It was also explicitly said to be able to hold the souls of demons and angels, and that apparently never happened since it just got destroyed already, so that seems kind of weird.
Take away the minutes on Azmodan's holophone and his Act would be pretty good. Instead of him telling us his plans, have it revealed by the panicked defenders of Bastion's Keep. Make all 7 of his SIn Lieutenants show up as bosses.
Act IV - No taunts over holophone from Diablo. Izual wouldn't be threatening us with the 'chill of Hell.' The lighting would get darker and darker as you progressed, signifying Diablo's corruption of the heavens. Nephalem wouldn't just randomly pitch him over the edge, either. Body dissolving into the soulstone and having the angels gather around it, uncertain of what to do, would probably work better, especially since a lot of people thought the Black Soulstone was destroyed at the end.
Act V - I kind of knew Malthael was coming back as Death, and figured his plan would be to kill all demons, so I liked where that went. No more telephoning in over the Black Soulstone to mutter 'Nephalem...' Their original plan was for Imperius to be the bad guy here and kill/gravely injure Tyrael, that makes a lot of sense and probably was what the End of Days was supposed to head towards since it began with the 'loss' of Wisdom, which the mortal Tyrael had become (which could be why the End of Days may not be referenced in Act V). Imperius, who voted to destroy humanity, working with Malthael, who wants to kill them for being part demon, makes a lot more sense than Imperius reluctantly helping us because Malthael for some reason decided to attack the Heavens.
Malthael definitely would not have shattered the Black Soulstone. He despised demons, so much that he was going to just straight up murder them all, even the innocent nephalem. The next expansion would still be able to continue with Diablo escaping anyway since we were told by Tyrael that the Black Soulstone was flawed and wouldn't be able to hold all the Evils for long, so they could have easily escaped without something facepalm worthy happening in the final boss fight.
Would the 2nd expansion be the final one? I don't know, but I would have it eventually come down to the demons and Man waging their final battle as foreseen by the Druids, probably with some incarnation of Tathamet as the final boss.
May be some other things I'm forgetting, but I think it definitely could have been more enjoyable if they tweaked how some of the events played out.
The treatment of Deckard Cain was so bad that one of my friends whose first Diablo game was 3 was even dumbfounded about how 'one of the most beloved characters in the universe' went down.
Leah should have been handled differently as well I think. You watch the Behind the Scenes thing (made before the game was out) and they all seem really proud of the character they created, and the betrayal of Adria was supposed to be one of the most evil things they could think of and you were supposed to be devastated about it, but it seems a lot of people didn't even care at all about her.
Definitely could have been a lot cooler; she's the daughter of Prince Aidan, a witch, and the Lord of Terror himself. Could have covered her learning that her father was the Warrior, and that she might be heiress to the bloodied throne of Khanduras.
They also hinted that rescuing her soul would be something they would pursue in the future (and the fact her soul is still out there is mentioned in-game by at least Covetous Shen), but I've glanced at the RoS spoilers and didn't see anything related to her (although it could be there and I missed it). Makes you wonder if they ditched that idea after seeing the reception she got, as the 'Reaper of Souls' expansion sure seemed like the place to deal with that issue.
Not to mention she was supposed to take over the 'Deckard Cain' role according to that Behind the Scenes thing as well.
Tyrael becoming 'black'/'Tyrone' is also one of the more bizarre ideas they came up with (Was there ever anything in the lore suggesting an angel or demon could strip away their own immortality? How is that even a thing?), and even worse that he then decided to take over Wisdom and remain mortal at the end.