While Junko is on the side of despair, she personally has no qualms using hope to further her despair. Also, no matter how you place it, Junko and her analytical prowess still make her a greater threat than Nagito because while Nagito's powers of luck are great, their effects are still unknown to him until whatever happens happens, Junko can rely on her abilities at any time.It's not really a rationalization of her evil. The idea that she is just entirely full of despair from her inception is still retained; in the end, the only thing Nagito would really do is to get the ball rolling. I'm just a big fan of the idea of the greatest threat in the series being a person who represents hope, and I think that goes well with how the game turns on its heads a lot of the characters and situations (such as finding out that the creator of the air purifiers created the Monokumas, discovering the truth of the Remnants of Despair, seeing that the Future Foundation is somewhat morally grey, Nagisa's father working for Hope's Peak Academy, etc.). I feel that having the true villain simply be Despair ends up just sticking to a script.
Ha has the belief that hope will inherently overcome despair. He also believes that hope 'eats' whatever despair it overcomes. As I previously stated, this is why he most likely joined Ultimate Despair and why he wants Monaca to become Junko II, because the bigger despair is created, the bigger hope will be after that despair is destroyed.You say that, but he literally almost made the new Junko, and is now trying to turn Monaca into a Junko who is more Junko than Junko ever Junko'd. For someone who can't do it, he was arguably more important than any character to start the ball rolling for Another Episode and, judging by the epilogue for this game, Danganronpa 3 may very well be driven in very large part by him.