Mahou Shoujo Madoka★Magica Movie 2: Eien no Monogatari

Commonalities in the introduction to the story. Protagonists of both works always judge their value from their actions in the story. Madoka goes through a time when agent can see the anguish in the expression of the characters, the same thing introduced in the context of Evangelion. 

Both of those anime are partially about time travel and it's consequences. Both are rather grimdark and sad. Both are excellent. If you liked the time travel theme of Madoka Magica 2 then you will most certainly like Steins;Gate. 

Shifting focus from a multiple character cast to maily two characters? Check. A further exploration of their personal experiences and the consequences of said experiences? Check. A further exploration of the connection these two characters have and how it affects their own lives & the existence of those around them? Check. Gorgeous visuals and quality fluid animation? Check. Fantastic cinematography and great directing? Check. A sequel that offers closure, yet leaves enough open for a possible future sequel? Check. Cute girls suffering? Check (let's be real, we can't deny it's true). Beautiful soundtrack? Check. [Sort of spoiler] Time-travel done right with a proper explanation of its rules and how it functions? Check. 

Both movies are the second in their respective movie series. Both anime deconstruct other anime from their respective genre, with Ideon being a deconstruction of mecha anime and Madoka Magica being a deconstruction of magical girl anime. Both shows feature young protagonists, who must use an unknown power in a battle against individuals from another race. They both have apocalyptic elements, as well as a huge number of casualties. Also, both shows have an overall similar mood. 

Both are mecha anime, which try to deconstruct their genre. In both anime, the main protagonist is a teenager, who becomes a mecha pilot, this becoming a child soldier in a devastating war. Both anime show the impact of war on these children, as they are forced to kill enemies and cope with the loss of their comrades. Also, in both shows, the main protagonists have a similar attitude and often refuse to participate in combat. Overall, both anime have a similar grim atmosphere and deal with similar themes. 

Both films have a history obsolete trying to explain the correct past mistakes. As in Kara no Kyoukai the protagonist Enjou Tomoe tries to understand what happened to his family and tries to fix the problem. What he does not know is that he is not a stuck temporal paradox created by Souren Araya. In Homura Madoka magika lacking in time and tries to prevent Madoka make the Contracted with Kyuubey. Trying to avoid that happened in the other timeline. Taking also both animes have as musical composition Kalafania. 

Both anime focus on young main heroines who have the power to travel in time. In both anime, the main heroine uses her time travel powers to prevent undesirable situations from happening, but discovers that the usage of her powers also has side effects too. Overall, both shows have similar concepts, as well a similar mood.