Really, Kuuga and Agito should be looked at as their own things. Agito obviously started out intending to be more of a follow-up to Kuuga, but it was something that was dropped in order for Agito to be its own thing. (The connection to Kuuga in those early episodes is pretty minimal, only using Kuuga as a segue to the G3 storyline.) While it would have been cool to have both shows take place in the same world, like the Showa Riders, I think it's for the best they split them up. (Although I feel like some of the holes with the Mysterious Youth is a result of breaking away from Kuuga.)
IIRC, Agito's producer, Shinichiro Shirakura, said that making Agito a sequel was heavily debated amongst Toei's staff, with a lot of people feeling like it would undermine Kuuga as a series, and specifically what Godai had accomplished in the series. And that's kind of true. I'm a fan of the Enokida character, and she busts her ass to invent stuff for the police, but along comes young hotshot Ozawa and makes Enokida's work obsolete? But by Agito erasing all connections to Kuuga, Enokida is again triumphant!