Both involve young girls forming a team to fight off invaders and protect the people. They also appear to be aimed at an entirely different audience at first but get progressively darker and more depressing.
Both are deconstructions of the magical girl genre and very cerebral. They both also have pretty strong sci fi plots, although the Alien 9 story in the anime doesn't really finish the story started by the manga. Both have excellent animation and some really well designed monsters, which contrast well to the very moe girl characters. Both of them are pretty damn sad and have some super surreal animation sections. Also, both of them are great and I love them.
Alien 9, like PMMM, comes off as an innocent and fun show at first, but slowly devolves into a story about mere children facing the reality of what they've gotten into. Both are extremely interesting to watch despite being " Cute Little Girls in Tragic Situations " shows.
Both series are a dark turn on the cute and moe genre that goes badly for the main characters, who are in both shows young girls. Both have a weird structure and plot twists and have unsatisfying endings, so its very likely that you will apreciate the other if you enjoy one of them. Also they are both extremely well done and dont give a damn about what the audience will be expecting.
Alien Nine reminded me of Haibane Renmei because of the level of bizarre and weirdness each of these shows contain. Both are out of the normal comfort zone, and have a slice of life with an interesting sci-fi twist.
Alien 9 is similar to Musaigen no Phantom World in it's main plot setting. In Alien 9 they are in a school club that fights aliens off their school grounds aided by Borg their alien helmets, Musaigen no Phantom World is also about a high school club that fights phantoms and use their special powers to their advantage. Though each show has a very different tone, Alien 9 is much darker and physiological whereas Musaigen no Phantom World is much more lighthearted.
Both anime feature extreme horror-themed violence, and both plots consist of a series of attacks by monsters which must be repelled by the series' respective heroins. Beyond that, they both feature very similar plots and general atmospheres with dark, overarching mystery-conspiracies that are slowly revealed over the course of the series. I would go so far as to say that Blood-C appears to have been very heavily inspired by Alien 9, but I cannot find a source that supports that claim.
Yuri and Tsubasa are both very similar.
a) They are child main characters with not the same ages but yet very similar ages.
b) They both have supporting characters to help them conquer their difficulties.
c) both have to fight aliens or enemies as little kids. It's their importance.
d) both cry a whole lot especially of dangerous things.
These anime both came out in the same year but I'd have to say Figure 17 was slightly more of a darker theme than Alien Nine, which contains more uncomfortable stuff for children more than Figure 17.
Both have VERY similiar protagonists, in that they are unwilling to do what they're meant to do, even though they have great potential.
Both are great looking series produced with amazing 2D animation. Emotional, touching, and psychological.
NGE has mecha, has a more layered and completed plot, has a symbolic ending, and is more mainstream and popular
Alien Nine only tells half the story, has a more honest approach with it's cast, subtly creepier, and is cuter.
Both take place in a school setting and have similar character art. Both have bizarre situations based on the sci-fi elements in Alien Nine and the overall comedic elements in Azumanga Daioh. If you like the weirdness in either one, you should watch the other.