The main problem with the story, even more than not building on the amazing ending of the first game, is that it's just so scatter-brained. It doesn't seem to know what it wants to accomplish. It's just Death running around, being an errand boy until the end just kinda happens.
The way I see it, these are the major points of the story:
1) Death feels a bit of guilt for killing off the rest of the nephilim. After ages of the Horsemen being the only remaining nephilim, he suddenly encounters Absalom/Corruption.
2) Death wants to bring back humanity so that War would be spared.
3) A conflict between the first two points: Death can bring back either the nephilim or the humans, but after he makes this choice, the other will be lost forever.
4) Lilith seems to be pulling Death's strings a bit. She - or whoever she's working for - wants him to reach the Well of Souls, and wants him to choose the nephilim.
The problem with the story is that maybe 1% of the game is spent focusing on these points. The rest is just Death running around and doing stuff because the game told you to run around and do stuff.
I feel like the story would have felt much more focused and satisfying if they'd changed just a few things:
1) Introduce point 3 much earlier. Not at the very end of the game, but more like the beginning. You go to meet Crowfather, he's crazy and turns into War and tries to kill you, you kill him. In his dying breath, he tells you to seek the Well of Souls, but that you'd have to choose between the humans and the nephilim.
Then they could have spent more time focusing on his inner conflict: Save the humans for War, or save the nephilim to atone for his past sins?
2) Lilith should've played a major role throughout the game. She should've basically played the same role Samael did in the first game, giving you help with your main quest, but clearly with her own ulterior motives. As her ultimate goal seems to be to revive the nephilim, I could see some interesting interactions where she'd try to push Death's buttons on the subject of the nephilim, subtly trying to sway his decision in that direction.
3) Absalom should've shown up earlier, and he should've shown up more often. Like you should've fought him two or three times throughout the game. He's a pretty major part of Death's story, so it's pretty lame that he only shows up like twice.
I could have seen the game going something like this:
- Death goes to the Crowfather. Crowfather is nuts. Turns into War and fights Death. In his dying breaths, he tells Death about the Well of Souls and how Death must choose between humans or nephilim. Then he sends Death to the Forge Lands.
- Death wakes up in the Forge Lands. He asks the Makers about the Well of Souls. They don't know shit, but if he makes it to the Tree of Life, he could go to other worlds and see if anyone else knows anything. But the way is blocked by corruption, so the forge needs to be repaired to create a weapon that can clear the way. So Death goes to repair the forge. But unlike the current game, this is just one dungeon.
- As Death completes the final step to repairing their forge, he's jumped by a big boss monster and kills it. Suddenly, Lilith appears. She tells Death that the creature was on her hit list, and asks Death if he wants to take care of the rest. He starts to blow her off, then she mentions that she knows how to reach the Well of Souls. She proposes a deal: Death takes care of her hit list, then she tells him how to get to the Well of Souls. Death accepts.
- Her first hit: the Bone Lord in the Kingdom of the Dead. Death gets the corruption-destroying weapon from the Makers and heads to the Tree of Life.
- As he arrives at the Tree of Life, he's drawn in and is suddenly in a fight with Corruption. Maybe this is a fight you're meant to lose. After losing, Death realizes that Corruption is Absalom. He then escapes into the Kingdom of the Dead - but by escaping, he also frees Corruption.
- Death meets Ostegoth, and learns from him that he can summon the Bone Lord's ship at Serpent's Peak. Unlike the current game, Serpent's Peak is a full-on dungeon. The amazing ship platforming sequence caps off the dungeon, and ends with a boss fight with the Bone Lord on the deck of his ship. MUCH more exciting and satisfying than the Bone Lord telling you to go kill his champion.
- The game continues with Death taking down Lilith's hits. Unlike the current game, this has you progressing through the worlds in a non-linear order. Not World 1, then World 2, then 3, then 4. But Dungeon 1 is in World 1, Dungeon 2 is in World 2, Dungeon 3 might be back in World 1, and so on.
- Throughout this, Death sees the damage that releasing Corruption has done, and occasionally interacts with him directly. Maybe expand on the corrupted angels concept. Have corrupt angels and demons working together. Maybe you encounter three-way fights between regular angels, regular demons, and corrupted angels and demons. Then instead of being the final boss, you take him down for good about two thirds of the way in.
- Lilith's final hit, and the game's final boss: Samael. However, he's grown too powerful in the present, so she sends Death to the past. Make that final dungeon much longer with much more elaborate past/present puzzles. And at the end, you find that Samael is still too powerful to defeat, so you end up imprisoning him - in the same prison that War releases him from in Darksiders 1.
- Immediately after returning to the present, Lilith transports you to the Well of Souls (which isn't in the Tree of Life). Final cutscene: Death makes his choice. He chooses War and humans over the nephilim.