Perhaps an ancient evil Saiyan who was banished long ago. This Saiyan would have powers that are unknown to Goku and Vegeta. He could be awakened from a deep slumber and is angry at the current state of the Saiyan race. He sees Goku and Vegeta as traitors for living among the Earthlings and decides to destroy them and take over the universe. His knowledge of ancient Saiyan techniques would give him an edge in battles against Goku and Vegeta.
Another option is a powerful demon from a different realm. This demon has been observing the Saiyans for a long time and is envious of their power. It decides to invade Earth and challenge Goku and Vegeta. The demon has unique powers like the ability to manipulate time and space, which would make it extremely difficult for Goku and Vegeta to fight. They would have to figure out a way to overcome this new type of power and defeat the demon.
Maybe a mad scientist - type character who has created a device that can disrupt the fabric of reality. He wants to use it to reshape the universes to his own liking. Goku and Lemon get in his way because they are trying to protect their respective homes. The scientist is constantly evolving his device and creating new threats for Goku and Lemon to overcome.
In a crossover with the Bleach universe, Aizen Sousuke could be a formidable antagonist. His intelligence and powerful abilities would make him a tough enemy for Goku. Aizen could manipulate situations to his advantage, and Goku would have to use his fighting instincts and newfound knowledge of this strange world to defeat him.
Maybe an old enemy of Goku's who has somehow managed to return. This enemy has heard about Goku Jr and figures that by attacking him, he can get revenge on Goku. This could be someone like Frieza who has found a new way to be resurrected and is more powerful than ever.
Maybe an interdimensional warlord who sees Goku as a threat to his conquest plans and Lemon as a valuable asset. He would stop at nothing to capture them and gain their powers. He could have an army of minions from different dimensions, making it really challenging for Goku and Lemon to fight back. This antagonist would be very cunning, constantly devising new strategies to outwit our heroes.
In some fanfictions, Vegeta could be under the influence of some external force. Maybe an evil entity has convinced Vegeta that kidnapping Goku is the key to achieving ultimate power. Vegeta, being power - hungry as he is, falls for it and kidnaps Goku. But later, he realizes his mistake and has to make amends, which can lead to an interesting story arc of redemption and friendship building between the two Saiyans.
Maybe it would be a combined form of some of Naruto and Goku's most powerful enemies. For example, if Frieza and Orochimaru somehow combined their powers and knowledge. They would be a very tricky opponent for the fused Naruto - Goku as they would know the strengths and weaknesses of both heroes.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
The Locust Queen could still be the main antagonist. Goku would see her as a great threat to the people of Sera. His sense of justice would drive him to take her on directly.
There's also the possibility that Orochimaru could be the main antagonist again. He might be intrigued by Naruto's new powers and try to experiment on him. Orochimaru is always after power and knowledge, and Naruto's Saiyan powers would be something he'd be very interested in. He could use his snake - like abilities and various jutsus to try and capture Naruto.
Vegeta would likely be arrogant towards Chibi Goku at first. He'd see him as just a puny Saiyan child. But Chibi Goku, with his innocent charm, might start to break down Vegeta's tough exterior. For example, Chibi Goku could offer Vegeta some of his food, which is a very Goku - like gesture. Vegeta would be taken aback but might slowly accept it. Then they could start to have simple conversations about their Saiyan heritage.