Perspective shifts and sides change, but there is quite a bit of time spent with the empire, which would technically make them the protagonists. The game ends differently than the first game, but if you continue into the DLC, you take over as the “evil” star killer & hunt down Jedi Leia. TFU2: You’re cloned by Vader, and again, are part of the empire. Half the game, the empire are the protagonists. If you kill Vader, you become the apprentice of the Emperor, which leads into DLC.
TFU1: Vader grabbed starkiller when he was a child.
Don’t remember the empire being protagonists in TFU games.