Orochimaru could be an antagonist in this fanfic. He is always seeking power and knowledge. If he gets wind of Naruto's connection to the Speed Force, he would surely try to either capture Naruto or find a way to replicate the power, causing trouble for Naruto and his friends.
The Akatsuki could still be the main antagonists. Even with Naruto having the power of the Speed Force, they would pose a significant threat. Their various unique abilities and their goal of collecting the tailed beasts would still be in conflict with Naruto's desire to protect the villages.
Maybe a new group of rogue ninjas who also have some connection to the Speed Force could be the antagonists. They might be jealous of Naruto's newfound power and want to take it for themselves, leading to battles between them and Naruto.
A jealous classmate could be a main antagonist. This person might be envious of Naruto's popularity and his ability to make friends easily. They could try to spread rumors or sabotage Naruto's projects.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
One possible antagonist could be a jealous noble from Naruto's own kingdom who feels that Naruto doesn't deserve the prince title. This person might try to undermine Naruto at every turn, spreading false rumors about him or trying to sabotage his diplomatic efforts.
Another possible antagonist could be a fellow inmate who has a personal vendetta against Naruto. Maybe this inmate was once on the wrong side of Naruto's actions outside the prison and now sees this as an opportunity for revenge. He could try to undermine Naruto at every turn, from spreading false rumors about him to physically attacking him when the guards aren't looking.
Another option could be Orochimaru. He has his own motives and is always looking for power. He could be the head of a powerful gang in the criminal underworld of the Naruto world. He would constantly be trying to capture Naruto or his friends to use them for his experiments or to gain more power over the ninja world.
The Akatsuki could still be the main antagonists. They might be interested in Naruto's tails for their own dark purposes, like using their power to create a super - weapon or gain control over the ninja world. Another option could be a secret group of rogue ninjas who have a vendetta against the Uzumaki clan and see Naruto's tails as a symbol of their power that they want to destroy.
One potential antagonist could be a new and mysterious organization that is similar to Akatsuki but with different motives. They might be interested in using Daisuke to open a portal to a different dimension or something like that. They would be constantly trying to kidnap Daisuke and force him to cooperate. Also, Orochimaru or his remaining followers could be antagonists. Even though Orochimaru has changed somewhat in the series, there could still be some of his followers who are more radical and want to use Daisuke for their dark experiments, believing that he has some special chakra or ability that could help them achieve their twisted goals.
There could be a new, mysterious force that is neither from the Naruto world nor fully part of the Olympian world. This force wants to disrupt the balance between the two worlds and sees Naruto as the key to achieving its goals. It could manipulate both sides and create chaos.
Well, in this fanfic, Naruto's use of the Speed Force could lead to some really interesting crossovers. Imagine him meeting characters from the DC Universe who are also associated with the Speed Force. He could learn new techniques from them or teach them some of his ninja skills. In terms of the Naruto world, his newfound speed could make him a more elusive target. He could use it to quickly gather intelligence across different villages without being detected, completely changing the power dynamics in the world of ninjas.
The villagers themselves could be the main antagonists. Since Naruto has been neglected, their continued mistrust and hostility towards him could drive his 'evil' turn. They represent the status quo that has failed Naruto, and he might see them as the source of his problems.