Personally, if I were to make an AA or SI, here's my general suggestions. A lot of these tie into each other, but I broke them up to make it less wall-of-text-y:
1) The character should change situations. If he/she doesn't, what the fuck is the point of them being in the story or for there to even BE a story?
Maybe the early and/or big events won't shift too much, but if you're going to insert a character, an impact must be made, even if indirectly.
Otherwise, you're just typing the fucking story into text format and what's the point of that?
2) The character should have flaws that do pop up.
I'm not talking about what I call Failed Flaws, where the flaw only comes into effect when it would be 'funny', causes them 'comically' falling into a girl's breasts, only comes up when it would affect NOTHING or give them an opening to a relationship, as it would simply become an advantage or even a moot point.
It's all right if they overcome some flaws, like a language barrier, crass behavior, an inappropriate laugh, etc. but make sure they have at least one that sticks with them for the entire story.
And being angsty and/or emo for a scene or two DOES NOT COUNT. That's just whinging in a weak attempt to fake a flaw. If it's going to be a flaw, it has to last a good long while and make people NOT want to associate with them.
3) If they're going to affect the story, then things will affect THEM. Whether it's serious (Seeing people die horribly, falling in love, needing to find a place to live, etc.) or fluff (making friends, getting a job, attending school), everyone reacts to situations.
And if they don't, they should be called on it.
4) A good character should be wrong or out-of-the-loop at some point and if they're going to be important, this should be the case more often than just once per story.
No one is perfect, and a well-done AA or SI shouldn't be either. Let them fuck up if they WOULD fuck up. Don't be afraid to have the character suffer humiliation or injury.
At the same time, don't make them a fucking martyr, as that's just as obnoxious as being perfect. More so, in my opinion, because why write a story if you just beat yourself up and focus on how miserable you are.
They should have their successes, even if one or two of them get blunted as not being all that important (i.e. they aced the interview and get the job, but it's nooot that great a job; or they defuse a bomb, but find it was a joke bomb that some asshole sent up to paint the school red; etc.)
5) Leave room for character growth.
Writing powerful/fully developed characters can SEEM fun, but it's NOT.
They should not start/remain at their pinnacle (unless you're going to strip that away or have them outpaced later in the story), and they should be allowed to evolve a bit, maybe refine skills or their personality.
And don't be afraid to give them quirks that never really go away. (and remember that quirks aren't flaws or advantages, they're just... 'quirks')
6) Don't relegate the main character to sidekick status.
It's all right if the AA or SI gets to shine on occasion, but remember that just like in any decent series, not every character gets to be the lead or even be all that important in every arc.
One of the biggest gripes about any crossover, AA, or SI is that the original main cast stops being important or is rendered pointless.
Why have Scooby Doo crossover with Bleach if Scooby and the gang can't contribute jackshit and stand around stating the obvious (unless you're using it as a comedic tool to poke fun at stupid crossover concepts and/or point out flaws in one or both series)?
Likewise, don't make the rest of the cast completely pointless to your story. If they don't factor in, don't make them part of the story.
7) It might be a good idea to create extraneous characters specifically to fuck with your AA or SI or even to create a balance between your AA/SI and the original cast, perhaps something that either of you can deal with, even if it's more often your problem than it is theirs.
And make sure that you balance these characters so that people other than your AA/SI can deal with them. It might be tempting to make it so your character is the only one who can deal with them, but it should NOT remain the case throughout the story.
Some people bitch about too many original characters, but really, fuck them. Using the original cast in places where you need someone doesn't work most of the time, and is usually insulting to whatever cast member could fit in that situation.
8) The character should have/develop a solid goal.
Even if it's as lame as wanting to help one of the main cast members through their emotional turmoil; as tired as trying to date a cast member; or incredibly difficult/time-consuming (become a legendary mage when they're struggling to cast a basic light spell), give them something to work towards.
