Densetsu Kyojin Ideon

Both very similar series not the the extent that it's extremely noticable, but EVA is much more heavy in emotion. 

Same creator, same concept. Densetsu Kyojin Ideon was the series Yoshiyuki Tomino did after Mobile Suite Gundam ended. It has the same setup: Teenage boy is the only one who can pilot the giant mecha. A group of humans are forced to leave their homes and wander space, always on the run from the same bad guys, go through personal stuff, etc. Teenage boy piloting the mecha must protect the group, with assistance from a handful of companions. It's a slightly different take on the character types and relationships, and the Ideon is made up of three separate component vehicles, originally created by some alien civilization. read more 

Another sick, sad, high-bodycount series by the same director. 

I'm really surprised no one has compared these here before. While the details of the similarities in plot are in spoiler territory, they have a lot in common. Both of them have similar wide reaching consequences and both of them have the same mecha related despair and slow realization that things are lot worse than initially suspected. The feeling of desperation and insignificance faced by the protagonists of both shows is very similar as well. 

Both shows are about conflicts between two humanoid races or factions, and their strange relation to a third party - a mechanical alien being, being revered as God with mysterious origin. Both shows also depicts the struggles of humankind, surviving in space, as well as the tensions between the Earthlings and the Settlers, tackled in a mature and serious way. 

The two are similar in many ways, and it's by the same author. There's also the fact that they both end somewhat abruptly, even though Zeta Gundam ended more properly and Ideon ended his story only in the movie which is epic. Both series aren't afraid to kill characters, that's a positive point. Even though it wasn't bad, I found Zeta's ending to be a little weak compared to Ideon's sudden series ending. 

Both are rather dark and trippy takes on their respective genres. Both have impressive audio and visuals (the Ideon Be Invoked movie at least, the TV series not so much) and pretty bizarre endings. It seems like Madoka is somewhat inspired by Ideon.  

Being chased across space with the crew being slowly broken down physically and mentally.  

You can't get more "Kill em' All" Tomino than these two ... both can be a hit or miss though, I personally didn't like Victory too much but loved Ideon. I'm sure many are different on that, or may agree, might love or hate both, etc! All in all though if you want brutally grim Tomino shows, these are it. 

Harlock and his crew are practically banned from Earth while they fight to protect it from an alien race called the Mazone, which resemble beautiful women in appearance. In Ideon the group who discover the "Solo Ship" and the Ideon end up being pushed away from their homeworld as well, with nowhere to run while being chased by the mysterious Buff Clan that resemble humans themselves. In both shows, the casts home is ... their spaceship, with nowhere else to go. If you can appreciate old art and animation it's easy to say both shows still look great to this day, with the exception of Ideon's recurring stock footage here and there. The Harlock series has better pacing and a much more likeable and developed cast all around, while Ideon is strikingly a bit more darker in tone and very desperate in nature. Both have incredibly impressive soundtracks, orchestrated and all. By the end of these two shows you yourself might be out of breath, as you'll feel like you went through these huge adventures personally. Typical of Tomino stuff Ideon is a little quirkier at times and has mecha, but overall the show is far more space drama than some of his other works. Overall, both have a lot of similar themes and ideas, with very different styles and executions in terms of writing/directing. But in the end these are two amazing, action packed, and adventure filled classic space dramas. And please note: Be Invoked IS the ending to Ideon. Episode 39 is just a sampler. read more 

Both anime feature a large cast of characters very quickly fleeing from dangerous aliens in a giant, mysterious, transforming mech to somewhere far away from home. The pilots and bridge personnel in each slowly figure out how to use their respective mechs more tactically while continuously running away and fighting a futile battle. Ideon focuses more on the effect that the relentless attacks of their alien assailants has on the crew. Meanwhile, Macross focuses more on how the aliens react and change after coming in contact with humans and their culture, especially music. So, for Macross watchers, give Ideon a look if you want something more pessimistic and grounded (Be sure to watch the movie sequel, Be Invoked, after finishing the TV anime). For Ideon watchers, if you wanted a more optimistic and lighthearted approach, go for Macross. read more 

Do you want peace or war? The question maybe is obvious to most, but it is hard to act on one's beliefs. What is more powerful, words or swords? What should one do? Or should one have faith in a giant?