How is it that Zoltun Kulle couldn't be killed by the Horardrim, but could be by us so easily? He didn't even do any of the things mentioned he was doing to them in the lore books (blood turning to sand, eluding them, casting curses on them, etc.). He just didn't seem to live up to that image of power (especially when his fight mostly involves dealing with adds instead of directly with him).
When you destroy the original soulstones in Diablo 2, it is said that the souls of the prime evils return to the Black Abyss where they were formed and it is implied that this is part of Hell from which all demons are spawned. In the book of Cain demons are formed from the husk of Tathamet, being the lands of Hell itself, and that the Black Abyss is some empty void of an area outside both Heaven and Hell, but it's still where their souls went after the stones were destroyed... Cain even describes how a black void opens to pull their souls in after the stones are shattered on the Hellforge. How the hell are their souls around in Sanctuary for Adria to "mark" so they will be absorbed into the Black Soulstone? The only ones that that makes sense for is Andariel and Duriel since they didn't have soulstones.
If the prime and lesser evil's souls were lingering in Sanctuary to be marked by Adria then why has everything been quiet for 20 years? They would have been up to their old schemes of corrupting mankind like they did before the Horadrim trapped them.
And how did Adria even track them down if they were capable of moving freely without being imprisoned in the stones? Surely they were all unwillingly captured in the Black Soulstone so how did they somehow get outwitted by this random witch?
Why is it that Diablo is the dominant personality in the Prime Evil? Is it because Leah was the Dark Wanderer's kid? Why does that really matter? Why doesn't he use the abilities of the other Evils more instead of just using a lot of his old moves?
Why did the final cinematic show Diablo's corpse falling and disintegrating when it was laying before us after we killed him? Every other time Diablo was defeated, his body morphed back into his vessel according to even the Book of Cain. So why didn't he turn back into Leah? And why was he falling anyway? Did they seriously just throw his body over the side or is that how his death really went and the corpse thing was just so there was something for the loot to spew out of?
Why did they allow the Black Soulstone to fall like that? It was stressed multiple times that it wouldn't be able to contain all of those powerful demon's souls for very long so they should have shattered it like Adria was faking to want to do, right? Wouldn't they all just be able to escape the stone and come back now?
What happens when something falls from Heaven like that? Does it really just fall down to Sanctuary? It's always been implied that Heaven and Hell are physically in some far-off corner of the universe far away from Sanctuary so that wouldn't make sense. It seemed like the only reason Tyrael fell to Sanctuary was because that is where he was intending on going after turning himself mortal. Would the Black Soulstone just be floating around in the emptiness of space now? In that case couldn't seven Evils just get out easily and make their way back to Hell?
Why didn't Diablo or Adria just kill Tyrael when they had the chance, and how do our characters just stand by and let this crap happen and where does she go and what does she do after Diablo is destroyed (again)?
I really hope some (if not all) of these things are addressed in future games/books (along with other loose ends like Malthael's whereabouts and the implications of a mortal Angiris Council member) and soon because the plot device of the Black Soulstone and its surrounding story elements didn't make a whole lot of sense...