Threre's enough threads about plot holes and inconsistancies. What I want to talk about is story delivery.
First of all I think that story is rushed: it seems that too much is happening and the events are poorly linked. Let's take introduction of Adria and the Black Soulstone. We're trying to help those who live in the city and then BOOM! 'I'm Adria, I worked tirelessly for 20 years, let's take Black soulstone and destroy Lords of Hell with it'. There's no lines about 'I don't think it's possible to kill Lesser Evils forever without Soustones', there's no doubt from Tyrael and Leah about Adria plan. But by that time we knew that she was one the leaders of the Coven who left it, also later we learn that she marked Lesser and Prime Evils so that they were sucked into Black Soulstone. Nobody asked why she did it. Also nobody asked something like 'Weren't Diablo, Mephisto and Baal supposed to die when thir soulstones were hattered in Diablo 2 and what was the point of placing their essences into another soulstone again?'
Imperius is Diablo's Arthas. He appeared in game 4 times. First time he was humiliated ty Tyrael, the second time he was beaten by Diablo, the third time he said to hero 'I will kill you but first I have to wash my socks', the fourth time he was going to beat hero but was defeated by Diablo again. So this charater looks very weak and almost comical.
Blizzard created great cosmology, gret story of the Eternal Conflict and Sanctuary. But why the hell everyone in the game knows everything? The Book of Cain is the great way to deliver story to players, I get it. But why was it recreated in game? It seems like Sanctuary is not medieval realm but the scientific capital of XXI century world. 200 years ago poeple did now know about Ancient Egipt, Babylon and other civilizations. 600 years ago people had very poor knowledge about the way people lived before them - just look at the paintings of the Bible events.
In many fantasy stories people know about Stone Age, evlotuion, etc. instead of having myеhs of religiuos beliefs about world and humans creation. There was no such knowldge during the Middle Ages.
So why did Cain knew everything about very ancient nephalem who were forgotten by the time of Sin War and were remebered only as gods? Why did he knew everything about Sin War although those events were erased from the people memory? Looks like it all is common knowledge in Santuary. What would be more logical is more more sparse information about ancient events which could be added by multiple sources. Enchantress could know something about legendary nephalem, Tyrael could tell about their power and how it was achieved by Uldyssian.
Also player does not need this information at all until almost an end of the game. It could be delivered in bits and pieces and just before the battle with Diablo angels could tell to doubtful hero: 'You're more powerful then both anges and demons because as nephalem descendant you're nephalem yourself . We can't beat Prime and Lesser Evils united in Diablo but you can'. Before that moment all what hero can do is within boundaries of human powers (Lesser Evils and Primes weakened by imprisonment in soulstones were defeated by humans in Diablo 2, there were no nephalem powers then since Worldstone haven't been destroyed yet), all the information hero needs is about Dark Exile and soulstones e.g. Horadrim information which Cain, Kull and Adria have.
Also I don't like quest flow. Why do we need to destroy Sin Hearts, why are our quest objectives changing all the time? Diablo 2 had a great approach: hero knew that he had to do something from the beginning of the act. He had to investigate Rogue Monastey, he had to find Tal'Rasha's tomb, he had to kill Diablo, Mephisto and Baal. There were no other main objectives, other characters just told the hero 'By the way, could you please find/kill something on the way to main objective? It could healp us greately'. Thats all. Only act 4 od Diablo 3 feels that way. Act 3 is close too except for quest for Sin Hearts. 'Empowering Baal's army with them'? Really? We could just be sent to deal with army leutenants, that's enough. There's no need in multiple quest objectives, just many make big zones with many mobs, and let us choose what to do - kill Big Bad Boy or help those who in need.
About atmosphere. There's almost no desperation. The story from hero point of view looks like 'well, we have some problems, people are dying, but I need to push forvard, kill some guys and everything will be allright'. And npcs mimic hero's words patting his back 'yes, you're mighty nephalem, you will do it'.
Also I have question about Archangels and Tyrael. They did nothing in game (except for that one time when Tyrael met his leutenant) without apparent reason. 'You must defeat Diablo alose I will just stand here'. Really? Also strange Auriel's imprisonment by demon? I though that Archangels are at least as powerful as Lesser Evils and could beat any other demon in combat.