 If you liked
Koukyoushihen Eureka Seven
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 ...then you might like
Kenran Butou Sai: The Mars Daybreak
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Put it in a nutshell, Mars Daybreak (MD) is a rough sketch of all Bones' anime features. And Eureka is a linear heir of MD. So they share lots of elements - a crew fighting against regime, an high-tech awesome ship (that thing did fly even though it's a submarine), mecha, teh genki shounen with brown hair, aliens and other stuff including graphics, orphans and a Green Peace spirit.
A merry band of pirates doing extremly reckless stuff. Thats what each anime does though eureka seven is in the air and mars daybreak's in the water.
They have a similar story of mecha pilot with great potential joining a single ship of rebels/pirates on alien planet.
pirate organisations with an anti-authority view and mysterious mechs? E7 and Mars Daybreak have got both these elements.
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Recommended by CtrlAlexDelete
While Eureka Seven takes place on earth and in the skies and has flying and gliding mechas, Mars Daybreak takes place obviously on mars and not so obviously underwater with mechas able to function underwater. Both shows are about a young boy who joins an organization and live in a ship. Both organizations are famous and have something to do with the government.