The second season of "Space Pirate Mito" takes on a somewhat more serious tone. it's still a late 90s sci-fi action anime, mostly geared towards a younger audience, featuring many simple characters and concentrating on people chasing each other around. Things that can be seen regularily on Cartoon Network – if not for some pretty "Japanese" twists, that are fairly common even in some anime for younger folks. In this Mito season the main storyline deals with gender issues and impossible (?) love.
The main storyline of the second season of the series (episodes 14–26) deals with the fact that Aoi has had a sex change. Then she/he falls in love with one of the galactic patrol siblings. It is Mutsuki, the female officer. Perhaps that's not your typical Cartoon Network stuff.
The downside to this drama content is a lack of congruity. As the main premise of "Space Pirate Mito" is a fun, brightly coloured action series with fairly typecast characters, those family problems and gender issues have a hard time being convincing in their own right. There's just too much other stuff going on, and the series doesn't look like a realistic drama series. So many of those traits fall flat. But for a viewer that can easily digest serious drama inside a "Flintstone" façade, this may well be a series for you.
Another series that, arguably a bit more successfully, mixes cartoon action with serious drama is "Strange Dawn".