That may be because Nagato didn't do nearly as much damage as Obito, minus destroying Konoha. But then he made up for it right after by reviving everyone and supporting Naruto.
Obito isn't evil deep down and obviously at this point in the manga isn't evil any longer & is trying to help Naruto. He is a good guy now. However, he still killed the 4th hokage, his wife, many body guards, and significantly lowered Konoha's strength. He killed many and destroyed various parts of Konoha w/ the Kyuubi. Those events led up to Naruto becoming an orphan and being hated and Sasuke's clan wanting to rebel against Konoha which in turn resulted in them being obliterated and Sasuke's sucky childhood. Then, he created a terrorist organization and manipulated Nagato, so he is actually indirectly responsible for Konoha being obliterated a second time. Then, he started a world war. When Nagato did things, it was according to what he wanted, he wanted mutual understanding through pain and suffering (which is wrong, but it's what he wanted so he did things according to that). Nagato wasn't evil, just misguided.
Obito wanted the Moon's Eye plan, but he did evil things that were not even related to it. He didn't have to attempt to kill Kushina after ripping Kurama out of her. He didn't have to have Konoha destroyed or manipulate Nagato into getting Naruto for him. He could have just kamui'd into Konoha and grabbed a child Naruto and left if he wanted Kurama so badly, innocent people didn't have to get hurt. But he chose other ways in which people would suffer. He was manipulated by Madara (which is understandable, he was a 13 yr old naive boy who was stuck in a cave w/ him for a year and had to listen to his speeches about how sucky the world was, who wouldn't go insane?), but due to that manipulation was evil during a certain point in his life. However, he is not genuinely evil like other characters, like Hidan, Kakazu, or even Deidara (yes Deidara was evil, or atleast psycho...he blew things/people up for fun and thought it was aesthetically appealing). Obito was evil for a purpose at times, and that purpose was to create an infinite illusion of peace.
