...posting in influences, I'd start my own topic about this.
Hopefully someone like Elhaym will post here, because she's a pretty avid fan of Evangelion.
Well, lately, I've been watching Evangelion (and while I still haven't seen the movie), I finished watching it, and I couldn't stop drawing parallels to Xenogears and saga. Mostly gears.
I'll have spoilers soon, but for a bit, I'll just talk about things that are not.
Kaji -> Citan -> Jin
Mostly, Kaji's voice and Kaji's "Quest for truth" throughout the series, as well as his looks. In, I think it was, Episode 18, Kaji is shown wearing a green bathrobe scolding Shinji and Asuka for fighting about The Fourth Child. He looked almost exactly like Citan in Xenogears, although he acted slightly more like Jin. Kaji is a spy for the Japanese government within NERV, just like Citan is a spy for Solaris's Government. Both reveal startling truths that make characters change their minds about... whatever, IE:
Kaji showed Misato the body of ADAM pinned down by Longinus on a cross in the NERV headquarters.
Citan showed Fei and Elly the truth behind the Soylent Systems, as well as Fei's psychological state. As a note, Kaji convinced Shinji to pilot EVA 01 against the thirteenth angel after he had run away again, just as Citan did with Fei on numerous occasions with Weltall.
Jin revealed the Y-Data's contents left in Canaan's brain, and exposed the truth behind the Miltian Conflict, letting everyone know about U-TIC and Joachim Mizrahi's lack of insanity. This is actually a lot more like Kaji than what Citan did.
Kaji's one interest is gardening, which Shinji found surprising when Kaji showed it to him in Episode 16? I'm not sure. Citan mentioned something about growing plants in Xenogears, and Jin undoubtedly worked as a gardener for at least some time =p.
There's another similarity between Kaji and Jin, but this would be an extreme Episode 3 spoiler, and I'll avoid mentioning it.
Ritsuko -> Juli Mizrahi -> Zeboim Era Elly(?)
Ritsuko's mother was the developer of the Magi Computer system (Three Sages of the East, also, Shevat's Sages), which she took over after her mother was killed by either Gendo or herself in her realization that she just killed a ten year old. Ritsuko is very troubled over what she is doing, and despised Rei because she knows about her mother. If not despised Rei, she is afraid of her, but from what she did to the dummy plug core, which was composed of Rei clones...
Juli Mizrahi's husband was the creator of the Y-data and tons of other amazing crap. Her husband killed himself after releasing the Gnosis, or was killed by U-TIC, or something, we're still in the dark about the details. She is afraid of MOMO just as Ritsuko's afraid of Rei, although for slightly different reasons.
Point is, both live in someone else's shadow and are both afraid of aritificial creations that caused the demice of the person in whose shadow they live in (or something similar like that, I'm sure you get it).
Zeboim Era Elly is a bit of a stretch, but you could still connect them. For example, Emeralda refused to acknowledge Elly as her mother, even though she did have a part in creating her. She isn't seen as important as Kim, etc. Although unlike Juli and Ritsuko whose "mentors" died before them, she died before Kim.
Toji -> Bart -> This is a very stretchy one, but in order to not reveal spoilers, I'll avoid mentioning the Xenosaga counterpart.
When Toji finds out Shinji is the pilot of Unit 01, he beats the snot out of him, but after him and Kensuke are rescued by Shinji during an angel attack, he forgives him, realizing that Shinji is neccessisary to protect Tokyo 3. He also becomes good friends with Shinji. His sister was sent to the hospital because during Shinji's first sortie against an angel, she was in one of the damaged buildings or something, and is seriously injured. He later on becomes an Eva pilot too, but is very reluctant about it, apparently he still has problems with them. Autopilot Unit 1, controlled by the dummy plug because Shinji refused to fight Toji's eva, eventuall nearly kills him, or, if the manga version is right, does kill him. He is the Fourth Child.
Bart sees Fei and Citan escaping from the Aveh Sand Cruiser (happens to be the only other one outside of Durandal too =p), he fights him and calls him a coward for escaping without rescuing his friends. After they fall into the stalactite cavern, him and Fei work together to get out. Fei eventually saved Bart and the Brigandier from Balthazar's gear's ambush. Bart and Fei become best friends later on. Much like Shinji's dummy plug destroying Eva Unit 04 and nearly killing Toji, Id, Fei's alter ego, nearly destroys the Yggdrasil as well as the Brigandier.
There's another one... but I won't mention him until Episode 3 comes out.
Rei -> Emeralda -> MOMO (Sakura)
Rei is an artificial creation, the core of the dummy plug, and I do believe Yui Ikari's clone. She is the pilot of Unit 00, the prototype Eva which has attempted to kill Ritsuko (or so it is assumed...). She doesn't seem to have many feelings, but is in fact, apparently, crushing on Shinji (her and Toji's conversation in Episode 18), and is trying to find purpose for her existance and is very confused. The only person she opens up to is Gendo, being a clone of his wife seems to be a good reason, to me. That, and the fact that he rescued her from certain death at the cost of his hands. She is also very expandable, as her clones power the dummy plug of Evas, and she gets killed twice, once by the hands of Ritsuko's mother, and another time by an angel which merged itself with Eva 00 and attempted to do the same with Shinji. Actually, the second time, was by her own will. She commited suicide to rescue Shinji, costing her her life, and most of Tokyo 3. Luckily, the city was empty.
Emeralda... well, she's also an artificial creation, and the first time you meet her, she attempts to kill you, just like Eva 00 tries to do to Ritsuko. The only person she really opens up to is Fei/Kim. That's all. She doesn't fill in as well as MOMO does. She's the only nanomachine colony in Xenogears, so she isn't replaceable, and I don't believe she was suicidal at any time.
MOMO is an artifical creation by Joachim Mizrahi. She stores the Y-Data and is the prototype 100 series realian. Like Rei, she is also a replica of someone else, in this case, Sakura Mizrahi. Sakura died defending Albedo from U-DO contamination while him and Rubedo attempted to heal her mind from the UMN Synchronicity virus. She attempts to destroy her mind during Albedo's hacking attempt (the second time, I'll mention this later), just like Rei does trying to protect Shinji. The Kirshwassers and 100 Series Realians are basically her replacements. Unlike Rei, MOMO has no trouble opening up to anyone who treats her with warmth, and unlike Rei she isn't very expandable because of her Y-Data, but aside from that, they're very similar. MOMO also tries to figure out her purpose, and whether or not she's worth anything, or just host a troublesome data.
On an interesting note. Albedo attempts to hack MOMO's brain twice, and both times leaves a piece of himself in her. Angels attempt to merge with Rei twice, the second time being succesful. The first time, interestingly enough, being the Eva that Toji was in that became an Angel. Earlier in the same episode, Toji and Rei had a conversation, and Asuka and Ekari (I think that's the girl's name) thought that they had some possible relationship. I found this interesting, because maybe Toji did like her, if even a little.
Shinji -> Fei -> Shion
The main characters, basically.
Shinji repressed tons of his memories of his father, has extreme self esteem issues, but still manages to be somewhat assertive sometimes. He is very clingy, or at least appears to be so, because of the abandoment issues. He doesn't want to attack Eva 04 because he sees an entry plug inside of it, and refuses to attack it and the possible cost of a human life. This ends up being a mistake, as seen in what I said about Toji. Anyway, he refuses to pilot an Eva numerous times throughout the series.
Fei has repressed tons of memories to the point of amnesia, also has self worth issues and is very assertive at times too. A lot more than anime Shinji, and slightly less than manga Shinji. Very dependant upon Citan, Bart and Elly to support him, just as Shinji is with Misato and Asuka, and to a lesser degree Kensuke and Toji. Fei's a bit more extreme than Shinji when it comes to psychology, as he has schitzophrenia, something Shinji didn't. He refuses to pilot Weltall several times, although that sub-plot is abandoned halfway through the Kislev Prison part of the game.
Shion's repressed memories are brought up throughout the Xenosaga games. We're still in the dark about most of it, and she still refuses to believe her parents are dead (see begining of Episode 1, Realian Clinic event), and her abandonment issues do not stem from either one of her parents, but from her brother Jin, although they're VERY mild when compared to the intensity of Shinji's. She has at least one breakdown in the games, and at least one during the anime (meaning there'd be a lot more to come). She's extremly clingy, at least to KOS MOS, and lacks the refusal to pilot anything like Fei and Shinji, but mostly it is because she has nothing to pilot other than a dinky AGWS which gets destroyed in the anime anyway. Of the three, she is the most assertive one, and is a lot less shy than Fei and Shinji, and I was having doubts of whether she belonged in this or not, but I guess she did.
Anyway, that's at least one way that characters in the series are similar.
I'd mention the symbolism too, but I am tired of thinking about this after coming up with all of THOSE, anyway. I'm sure I could tell you stuff like, how Gendo and Grahf relate, where Fyuiyutski comes in here, Yui Ikari, etc.