The main antagonists could be the Sith Lords who are secretly pulling the strings during the Clone Wars. Even though Luke is from a later time, the Sith's influence on the Separatist movement is still a major threat. Darth Sidious, in particular, would be a huge obstacle for Luke. He has his own plans for the galaxy, and Luke's presence could disrupt them. So, Sidious would likely send his minions after Luke and try to eliminate him.
One possible plotline could be Luke's discovery of a long - lost Jedi technique during the Clone Wars. Maybe he uncovers it while on a mission to rescue some clones. Another could be his interaction with famous Clone Wars era characters like Anakin or Obi - Wan. He might learn valuable lessons from them that shape his future as a Jedi.
In many of these novels, the remnants of the Galactic Empire are the main antagonists. For example, Grand Admiral Thrawn in the Thrawn Trilogy. He is a brilliant military strategist who poses a great threat to the New Republic that Luke and Mara are part of.
Maybe the old Imperial warlords who are against any kind of reform. They are used to the old ways of the Empire and don't want Luke and Mara to change things.
It could be a group of power - hungry humans who see the Laguz as a resource to be exploited. They might want to use the Laguz's unique abilities for their own gain, like using their strength in labor or their magical abilities for warfare.
It could be a new group of rogue ninjas who have a vendetta against Konoha. They might be led by a powerful and cunning ninja who has a personal grudge against Naruto or the village in general.
The Emperor could still be a major antagonist. Even though Anakin turned on him in the end, his influence might still be felt. He could send his agents to try and find baby Luke to eliminate any potential threats to his power.
Obviously, Darth Vader is one of the main characters. He is the central figure whose actions and decisions drive much of the story.
The Sith, definitely. They are always the main antagonists in the Star Wars universe, and in this fanfiction, they would be the ones trying to keep Anakin on the dark side. Palpatine, in particular, would be a major antagonist as he was the one who manipulated Anakin in the original story.
It's hard to say without more details about the fanfiction. But it could be some characters who benefit from Teddy not having rights, like power - hungry individuals or those with prejudiced views.
Another possibility is a group or organization that has different ideals. If Thalia and Luke are part of a group that values something different from them, that group could oppose their decision to have a child and become the main antagonists, trying to stop the pregnancy or take the baby away once it's born.