Madara could also be the main antagonist in a different - turn 'naruto return to past fanfic'. If Naruto changes things in the past, it might disrupt Madara's original plans. Madara, being a powerful and ambitious character, would not take this lying down. He could become more aggressive in his pursuit of the Eye of the Moon Plan and Naruto would have to face him in a new set of circumstances, making for a very different and exciting story.
It could be a new villain who has been plotting against Konoha while Naruto was away.
It could be the Akatsuki. Since Naruto is now following a more Sasuke - like path, he might attract their attention more. They might see him as a potential threat or someone they can manipulate, just like they did with Sasuke.
It could be a rogue ninja who took advantage of the chaos during the war. This ninja might have been gathering power in the shadows and now sees Naruto as a threat to his plans.
Well, the obvious choice would be the Joker himself. His return could mean he has some new and devious plan to wreak havoc on Gotham. He might be more powerful or have some new allies this time around.
It could be a time - traveling enemy from the future who wants to stop Naruto from changing things. This antagonist might have his own motives for wanting the future to remain as it was, like having power over a ruined Konoha.
Perhaps a powerful figure in the Naruto world who senses Naruto's newfound memories and abilities from his past life and sees him as a threat. This could be a rogue ninja or even a hidden power within the ninja villages. They might try to stop Naruto from fully exploring and using his past - life powers.
A powerful rogue ninja who has mastered a forbidden jutsu that gives him the ability to control minds could be a great main antagonist. He could use this power to turn Naruto's friends against him, creating a lot of internal conflict within the group.
Perhaps an old enemy of Itachi's from his past who has also reincarnated or found a way to exist in the modern day. This antagonist would try to use Naruto's kids as a way to get revenge on Itachi, seeing them as a weak point in Itachi's new - found role as a protector.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.