In Episode 1, Lila disguises herself as Captain Ryuuya to get onto the Timeship and make sure the Londarz Prison gets pushed in. But what happened to Ryuuya? Simple: he let her go ahead with her plan. Why? It's revealed in his final moments that he saw two futures when on the V-Rex and thoughout the series, he knew just what was going to happen in the past, changing certain events like the Timerangers surviving their first giant monster battle so his original death wouldn't happen. When Lila tried to restrain him, he knew it would happen so he played along.
Naoto and the other Timerangers had Identical Strangers in the finale. The Timerangers are not from the present timeline so it's OK. Naoto, on the other hand was Killed Off for Real, and it's stated that he doesn't have a twin brother.