It sounds like the annoying things the player does are all in-game and characterization related rather than meta-game related. What I mean by that is that the player isn't having his character stop the other party members from doing anything or even engaging in manipulative behavior to minimize the importance/screen time of the other PCs. The player is fine; his character's just a jerk. It sounds like he's already making sure to be party-focused and 'aids the other characters', but the way his character is a jerk is a problem for you, particularly since he appears to you to be flawless.
If this is the case, there's one thing you really should be doing:
Run scenes that aren't plot-critical! You should be doing this anyways if you have a character-focused playstyle, and especially in Anima; you're missing like 9/10ths of the cool setting stuff if you don't take the time to run the things that aren't at all related to the current plot. There's just so much stuff, and most of it can't be important all at the same time. Run the characters having dinner, or going to a Church-sponsored party, or working a day in a soup kitchen, or having a deep and meaningful existential conversation, or whatever.
This will help with the current player, because the problems you mention can't come up in such scenes. You can't steal the spotlight in having dinner or, if you do, the characters should react to it and not invite him to the next one (In that case you should run-- very briefly-- the lone character's dinner separately from the group's somewhat longer scene. This can be hard to do right). People who try to steal the spotlight in every scene do exist in real life, and eating dinner with them is not fun. Deep conversations are even better, because they should naturally just stop when the problem character is around.
Basically, these scenes should illustrate that the party is growing together and becoming a close-knit loving community, and that his character is being excluded from that because he/she's a pain to be around. A really good person, but still a pain. The party still works together, and he/she's still part of it, but it should be clear to him/her that he/she's missing out on this great relationship which, given the character, should also be missing from the rest of their lives.
Alternatively, maybe the character is only like that in-mission, when actual heroic behavior seems to be called for. In that case these scenes should be great fun for everybody and help make the character seem like a minorly flawed hero (he's still insufferable when you make a moral mistake) rather than a tragically flawed one. Hopefully you'll even come to not-hate the character yourself!
In a 2-person game, this is harder. You don't have the other PCs as a sort of constant contrast to the character. You will need to make the more detailed NPC relationships fill that gap. The character should go through one of the following processes, if you do things right (depending on what the character is actually like):
1) is a insufferable jerk
2) realizes that they're lonely
3) tries to have people, and fails because is an unsocialized insufferable jerk
4) works really hard at learning how to not be a jerk, possibly with the help of NPCs
5) character is no longer an insufferable jerk, and has grown and matured in cool ways; character is kind of awesome.
1) is an insufferable jerk when it comes to other people making the wrong choices in heroic situations.
2) doesn't work well with others. That's why they work alone.
3) not a bad person to be around, outside work
4) this aspect of the character does not undergo character growth in a one-player campaign. Character may be cool, but this is unlikely to contribute with out special attention paid to it. On the other hand, this is also unlikely to cause you problems in the two-person game.
Addendum:
You may just really not like this kind of character, even with the modifications to play suggested above. In that case, you'll have to help him make a different kind of character.
To do this, give him restrictions on what kind of character he can make, something like "two quirks and a flaw", and build the character with him. Don't help so much with mechanical stuff, focus on making sure the character's personality and backstory will work for you. Let him do the content generation, but explain what you do and don't like about anything he suggests so he can come up with a character you're both happy with.
