It could be an evil time - traveling sorcerer. He wants to rewrite history in the prehistoric era so that he can rule the world in the future. He sees the Dino Thunder Rangers as a threat to his plans and tries to stop them from interfering.
A powerful alien being could be the main antagonist. This alien has been observing Earth's history and decides to interfere in the prehistoric era. It plans to use the power of the dinosaurs to create a weapon that can be used to conquer other planets. When the Dino Thunder Rangers arrive in the past, they become the only ones who can stop this alien's evil scheme.
Maybe it's a rogue Dino - like creature from the future that got sent back in time on accident. But once in the past, it decides to take advantage of the situation and become the ruler of the dinosaurs. It starts causing chaos and the Dino Thunder Rangers have to stop it.
In a 'Dino Thunder Back in Time' fanfiction, the story could start with a strange time - warp device malfunctioning. The Dino Thunder Rangers find themselves in the past, during the time when dinosaurs ruled. They soon realize that their presence is causing disruptions in the natural order of things. They meet a group of dinosaurs with unique abilities that are being hunted by an ancient evil. The Rangers decide to protect these dinosaurs and use their knowledge of modern technology (in a limited way) and their Dino Thunder powers to fight the evil. Along the way, they make new friends among the dinosaurs and early creatures, and eventually find a way to fix the time - warp and return home, but not before leaving a positive mark on the prehistoric world.
Cell could be a great antagonist. Even if Gohan goes back in time, Cell might still find a way to exist. Maybe he adapts his plan to absorb the Androids earlier in time. Gohan would then have to face a more powerful and unpredictable Cell, who could potentially change the timeline to his own advantage.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.
Well, there could be a crossover where the villains from Dino Thunder and Dino Charge join forces first. This would force the Rangers to put aside their differences and come together. The Dino Thunder Rangers might be a bit skeptical at first about the Dino Charge Rangers' methods, but as they face tougher challenges together, they start to respect each other. And perhaps there could be a love story between a Ranger from Dino Thunder and one from Dino Charge in the fanfiction, adding a bit of romance to the action - packed adventure.
An old rival of Dino's from his past could show up. This person might have a grudge against Dino and decides to target Hibari as a way to get to Dino. Since Hibari is so proud and strong - willed, he doesn't take kindly to being used as a pawn, and together with Dino, they have to face this old enemy. This antagonist could have some powerful fighting abilities or some dark secrets that make it difficult for Dino and Hibari to defeat him.
It could be a time - traveling version of Orochimaru. He might have his own plans for the past and Sasuke's interference could put them at risk. So, he tries to stop Sasuke from changing the past in a way that would undermine his future goals.
It could be a time - traveling version of Zeref. He might be trying to stop Natsu from changing things in the past that could potentially lead to his own downfall in the future.
It could be an ancient and powerful Titan who was thought to be defeated long ago. Since Percy is in the past, this Titan could be in his prime and see Percy as a threat to his plans of ruling over the world again. For example, Kronos might be even more powerful in this past era and Percy has to find a way to stop him without the help of his modern - day friends.
Madara Uchiha could also be a main antagonist. If Naruto goes back to a time when Madara was still alive and plotting, Madara would surely oppose Naruto's attempts to change the future. He has his own grand plans for the world and wouldn't let Naruto interfere easily.
It could be Danzo. In the original story, Danzo was a major factor in the Uchiha massacre. If Itachi goes back in time, Danzo would likely still be plotting against the Uchiha. His thirst for power and his extreme methods would put him at odds with Itachi's new attempts to save the clan.