Tatsuya's and Yuri's feelings for each other. They develop slowly throughout the whole series and it feels really nice.
Also, Domon and Honami, who had a son together.
Episode 4: When Tatsuya expresses amazement about Sion being alien, Domon insists on Tatsuya calling Sion by his species' name, pointedly stating that humans are aliens to other species. A very nice reminder that all life is equal, no matter where you come from.
Episode 35 is full of these. We have the Timerangers visiting children at a hospital. There's a boy who is Naoto's fan, but our aloof Sixth Ranger said he wouldn't go there to see the kid. By the end of the episode, there he is, supporting the boy who's about to undergo surgery and seemed confident after being supported by his idol.