Although you have the crazy minority fringe who say Hades Did Nothing Wrong, I think most people appreciate him as
a villain an antagonist because they can relate with him, not necessarily because they felt he was justified in everything he did.
You do feel bad for the guy, because at the end of the day, he legitimately does just want Amaurot back without any ulterior motives other than missing his friends (unlike Hahabread and Elidibus). And he is more morally conflicted than he lets on; if you read Tales from the Shadows, as Solus, he was basically ready to say "fuck it" and desert the Ascians before his son/Varis's father died.
Simultaneously, the game demonstrates that he does need to be put down, as he's given several opportunities at redemption and passes on all of them:
- After his son died, he could have put his hope in Varis, who very obviously craved his approval and love, but instead he turned cold and abusive
- He could have let G'raha sacrifice himself to save the WoL, but the only way the WoL is worth anything in his eyes is if they can shoulder an entire continent's umbral aether by themselves.
- When Ardbert merges with the WoL, and Hades briefly sees the WoL as the Amaurotine that they were before the Sundering, he chooses to ignore it and pass it off as an illusion, despite the fact that he was probably the second-most talented Amaurotine that ever lived (behind Hythlodaeus) at being able to see souls and aether.
He's a good character in that he is probably the most relatable, human Final Fantasy antagonist that Square has ever put in a mainline FF game. The tension (your feelings for his plight versus the knowledge that you can't let him go on with his plan) was what made him so enjoyable. He's probably not my favorite--that honor probably still goes to Kefka--but he's damn close.