I dunno if anyone will see it though. Anyway... Is it possible for agents to find and recruit a character if they are only briefly mentioned? Would said character even come into existence within the badfic? Say it were something like...

"Whos that" fluttershy asked?
"Oh" Twilight replies "Thats my sister. We have the same colors but our manes are a bit different. You could have seen her around and thought she was me"

(And, yes, intentional writing mistakes for that authentic bad fanfic feel.)

I posted a workshop/rant/thing a while ago with various tips and tricks for making characters (or at least, how I go about the process). The original post has been well and truly buried, but you can still read the information here. There's also a follow-up regarding characters with powers.

If you still have any concerns while creating your character, get someone else to look at what you have. A second set of eyes can be helpful, or at the very least get you to notice something that you might have missed at first glance.

That means, first and foremost, that in terms of personality, relationships to each other and others, and the way they act in missions, they should be interesting - not necessarily likeable, but interesting. You should also plan for character development of some kind, whether it's a major change in the character, or simply your team growing to work better together. Again, character development needn't be positive - my Agent Dafydd gets more and more power-mad as his series goes on, ending in his death (and resurrection).

Secondarily, or tied into the above, is choosing what you want them to be. There's absolutely nothing wrong with having two normal human teenagers/young adults - it's the classic setup - but you may decide you want something else. Badfic recruits are fairly common, as are characters who just joined up from their home universe, whatever it may be. And the species and background of a character will influence what you do with them.

The reason I say this is secondary is that it's all to easy to make a character you think would be awesome - let's say a Mandalorian bounty hunter who becomes a Jedi, then falls to the Dark Side, gets a cybernetic arm, and then reconverts and runs off to join one of the various Force cults dotted around the Galaxy Far Far away - only to discover that you either a) write them as if they were a human teenager, b) make them little more than a textbook of their own backstory, or c) give them so many powers that they never have to work at anything. If you know beforehand that you want to write, say, a fall-and-redemption story, then you can make a character to fit that (in this case, cut out the re-conversion and have her switch straight to the cult, so she can slowly regress to Sith methods before finally being redeemed and remade as a Jedi - or a dead Jedi).

There are no actual 'guidelines', because everything depends on the writer. What might be an overpowered Mary-Sue in one person's hands could be incredibly well-written in another's. Just remember: agents are supposed to have a difficult job, so don't keep adding on things to make it easier. And be aware that Phobos and Neshomeh will ask you why every single trait exists. ;) (Sorry, guys, but it's true!)

And yes, it's fine to have multiple agent teams. However, given that most people who get Permission end up writing one mission and then vanishing off the face of the Board, it might be better to start with one to avoid overloading yourself. :D

hS