It doesn’t appear likely that Rip will become a villain and represent the core threat of the season, as the show has already gone down that road with the Legion of Doom arc.
The reason for this is the fact that we will see two captains locked in a battle of ideologies.
That said, it’s becoming increasingly apparent that decisions made at the beginning of Legends of Tomorrow’s third season — which almost definitely involve dinosaurs — will have enormous effects that will set the tone for the rest of the season.
With Rip leading his newly established Time Bureau in a “by the book” manner, and Sara opting for a looser (and arguably more reckless) modus operandi, the show has built towards a conflict between these former teammates.