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.
Anakin, on the other hand, has a complex history. He was once a great Jedi, then fell to the dark side and became Darth Vader. In this fanfiction, he is in a redeemed state or perhaps a state where he is still grappling with his past actions. His presence in the story is crucial as he is the father figure that Luke has been seeking to understand.
The main characters are Anakin and Luke. Anakin has this whole arc of being a Jedi prodigy, falling to the dark side, and then potentially finding redemption. Luke is the one who has been on a journey to discover his heritage and become a great Jedi. When they meet, it's like two parts of a story coming together. Their different experiences with the Force, their relationships with other characters like Leia and Han, all these elements can be explored through their encounter in the fanfiction.
One possible plotline could be Anakin, in a redeemed state, secretly protecting baby Luke from the remaining threats in the galaxy. He uses his remaining Force abilities to shield Luke from danger without revealing his identity.
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.
Often, Palpatine can still be a main antagonist even in time travel fanfiction. If Luke and Leia travel back in time, he might sense their presence and try to stop them from changing things that would undermine his power. Another could be Darth Vader if they travel to a time when he was still firmly on the dark side. He would be a powerful foe for them to face.
Sith cults could also be antagonists. They might sense the power of the unborn child in the Force and want to turn it to the dark side. They could launch attacks on Luke and Mara to either kidnap Mara or influence the unborn child through dark side magic or the Force.
It could be the Volturi. Since the baby is a vampire - human hybrid, the Volturi, who are very strict about vampire laws, might see the baby as a violation of their rules and try to eliminate it.
The Foot Clan could be a main antagonist. They might see the baby sister as a way to get to the turtles, either by kidnapping her or using her to blackmail them. Another could be Shredder himself if he returns. He would surely not pass up the opportunity to use the baby sister against the turtles. And Baxter Stockman could also be an antagonist. He might be interested in using the baby sister for some of his mad - scientist experiments.
There could be a rogue Saiyan who has different ideals from Vegeta. This Saiyan might think that the baby should be raised in a more traditional, warrior - like way and try to take the baby from Bulma and Vegeta. Or, an evil scientist who wants to experiment on the baby's unique Saiyan - human DNA could be the main antagonist, creating all kinds of challenges for Vegeta and Bulma to protect their child.
It could be some rogue shinigamis who oppose the idea of rukia and ichigo having a child together. They might see the baby as a threat to the existing power structure in the Soul Society.