It could be Orochimaru. He is always interested in powerful ninja and their abilities. If he hears about Naruto's little sister and her potential powers, he might try to capture her for his experiments. Also, some of the traditionalist ninja in Konoha who are against Naruto because of the Nine - Tails might also see his sister as a threat or an outcast just like they see Naruto, and could oppose her in various ways.
The Akatsuki could be potential enemies. They might see Naruto's little sister as a way to get to Naruto. Maybe they think they can use her as a hostage or extract some information from her about Naruto or the Nine - Tails. Another enemy could be some of the rogue ninja who are after the bounty on Naruto's head and see his sister as an easy target to get to him.
His friends like Sasuke and Sakura could be his allies. Sasuke might be initially skeptical but then see the potential of Naruto's arcane power in fighting common enemies. As for enemies, Orochimaru could be interested in Naruto's power for his own experiments. He might try to capture Naruto to study and steal his arcane abilities.
The Akatsuki could be potential enemies. They are always on the lookout for strong ninja to either recruit or eliminate. Since Kakashi is a well - known and powerful ninja, his little brother might draw their attention. They could see him as a potential threat or a valuable asset.
The Akatsuki could be potential enemies. They might see the Mokuton Prodigy as a threat or a valuable asset to capture. Their diverse powers and motives would make for interesting confrontations with the prodigy.
A group of bandits who operate near the village could also be enemies. They might target Naruto Jade's dad because he is a threat to their illegal activities. They could try to ambush him or attack the village to get to him.
One possible plot could be that Naruto's little sister is also a ninja in training. She might struggle with the same kind of ostracism Naruto faced because of the Nine - Tails inside him. However, she could also be a source of great support for Naruto, helping him through his toughest times and together they could train to become stronger. Maybe she has a unique ninja ability that even Naruto is in awe of.
The people who previously neglected Naruto could become his enemies. They might see his new - found power with the Keyblade as a threat.
Potential allies could be his friends like Sasuke. Sasuke, with his sharingan and combat skills, could team up with Naruto in battles against those who fear Naruto's newfound genjutsu power. Enemies might include Orochimaru. Orochimaru is always interested in powerful abilities and would likely see Naruto as a threat to his plans.
Allies would definitely include Naruto's closest friends like Sasuke and Sakura. They would stand by him even with his new identity. From the Dragon Ball world, Goku could be an ally as he has a good relationship with Beerus. Enemies could be those who want to use Naruto's connection to Beerus for their own evil purposes. For example, some rogue ninja groups might try to capture Naruto to bargain with Beerus. Also, any new villains introduced in the fanfiction who are jealous of Naruto's power would be his enemies.
Well, obviously Naruto himself would be a main character. His sister could be an original character created just for the fanfiction. In terms of the harem members, Sakura could be one. Even though she has feelings for Sasuke in the original series, in this fanfic she could see Naruto in a new light. Hinata is also a likely candidate as she already has deep feelings for Naruto. Another could be Ino, who might be drawn to Naruto's growth and newfound confidence in this alternate scenario.
A new friend for the little sister from outside the Lab Rats' world. This character could introduce her to normal teenage life things like school dances and homework, which would be a contrast to her life as part of the Lab Rats' family. It could also create some internal conflict as she tries to balance both aspects of her life.