First suggestion: Read this.
Second suggestion: Write yourself as an agent. Write yourself as being a new agent. I'm a bit unsure as to why there was a move away from this, because overall it lends to more than a few things, such as the fact that you're immediately able to get into the swing with yourself rather than making an agent especially for the PPC and thus ~*~perfected~*~ for being an agent, and two, it lends credence to when you're writing your first missions and you have no idea what you are doing. Because, believe me, you don't.
I read all the missions and every bit of supplementary information out there when I was new and I still had no idea what I was doing when I started my first mission. Is this funny? Is that funny? Am I doing this right? Can I do this to her? Is it okay if I break all these things terribly? What the hell is even going on here? Oh God, help, I think I just lost where the Sue is?
But it was okay, because I worked that in with my agents, because they didn't know what they were doing either!
That doesn't work out so well when your agent has been around for over five years, is a tough and hardened veteran of the Sue Invasion of '08, carved a macrovirus off their partner's face, was around for Crashing Down and Reorganisation and so on...+ (It is easier to blame the goofs on your agent not knowing what they're doing- and it's funnier- than if it's an agent that should know what they're doing. Cluelessness is funny. Incompetence at a certain point is just sad. Especially when they're being touted and held up as being a pro.)
Beyond that, remember, you are working not with two individual characters, but with a pair (usually). Agents working in pairs allows for dynamism during a mission. Depending on which Flower paired them up it could be because they balance each other in such a way that they're able to perform their duties, it ensures that agents are learning from each other in ways that will improve their future performance, or because it's a mean and sadistic move making two people have to work together even though they drive each other up the wall.^ It allows for actual character interaction. After all, one agent by themself? What if their weak spots are involved? If one agent is able to keep calm and carry on, and the other can't at a particular spot of the fic, it gives us something to enjoy beyond just the sporking, and serves as reminding us that they are balanced.
Next item. We enjoy humor here. We also have an eye towards serious stuff at times as well. That said? Your agents should be characters in their own right. They shouldn't be made up perfect for just the PPC. They should be able to function elsewhere. In theory. Why? Because a good character is more complicated than shouting out random things just because, or being able to shoot a Sue with a clever wittism. They need to be interesting. At the same time, it's about knowing what you are able to write- and you need to have an eye for both.
Know what sort of humor you're going to go for. Know what sort of jokes you like that you are able to write well. What sort of humor is your character able to provide? If it's dead baby jokes ("Your baby was crawling all over the place!" "Oh dear, I'm so sorry, were you able to get her to sleep, at least?" "It's okay, I nailed her to her bed! She's not moving anywhere!") they probably won't work out too well.* If it's running around being random (Screaming "POTATO! POTATO!" constantly for no real reason beyond thinking that 'potato' is a funny word°) that also might not work out. Don't forget, timing is everything, too. A joke can quickly become awful and inappropriate if it's given at the wrong spot. If your character doesn't actually have comedic timing, that can turn bad really quickly. Knowing how to write something that is really, well and truly funny is important for the PPC.
Know what's creepy. And then? Avoid it. It's not funny. It's not anything beyond severely discomfiting to people. The guy who stares at all the female agents' boobs and molests unconscious female canons when they're knocked out or out of it because hey, he has a neuralyzer? That's creepy. That's not appropriate. That should make you feel icky just thinking about it.
Know how they're able to be serious. What do they get serious about? How do they act? Will they be serious all the time in a place like the PPC? If they are, it's not much of a problem- if they're paired with someone who will be cheerful about doing their job and enjoys it and has no problem being an annoyance to their stuck-in-the-mud partner. Otherwise, you might need to reconsider. Are they mostly level headed? What makes them go into a panic, then? What makes them angry and forget about trying to be reasonable? What makes them dissolve into laughter for several minutes? And if they're constantly being chipper and happy and constantly making jokes or having fun, what makes them stop laughing? What makes the smile drop from their face? What gets them to act serious?++
Do they have any tales of dark, terrible woe behind them? You might have to reconsider it.^^ The PPC is a hard place, in its ways. I mean, we're talking about a place where you're fighting things that are out to destroy worlds on a day to day basis! Missions fail! People die! It's a job that drives people insane! You get no pay, no recompense beyond knowing you're doing a job that helps the multiverse. You need to be able to grin and have a laugh- at something, anything. Missions aren't fun to read, point blank, if it's as dark as dark. Existential angst isn't a good idea. Suicide (no, not him) doesn't really have a place here, unless it's played for a laugh, and I'm not going to go into the details as to why that can be a bad idea. Abuse doesn't belong here. Sexual harassment. Rape. These things go along with the PPC itself- not the missions- about as well as jet fuel and your liver do. There are ways to involve these things, of course, because with competent writing anything is possible, but for the most part, you- this is a general you- aren't able to play it off. The moments where these things are appropriate to bring up are rare, and should be kept rare. (Please note: This paragraph is with regards to these subjects in the PPC itself, rather than as part of mission material. There is a difference between what the PPC has, and what the contents of the badfic we deal with has, and how it is dealt with.)
In short, keep it simple. Write who you know (which is usually you). Write to your knowledge level (you don't know what it is and how to deal with it in a good way until you've worked with it yourself, because you write different from everyone else!). Know how you are going to approach things- a character that makes rape jokes probably shouldn't be in the PPC. Nor should one that has a terrible awful past that she can't help but bring up all the time. They also need to have the capability to be serious (because sometimes, it is necessary.)
+This is a Stu. Or a Sue. Yes, as an agent. In the PPC. And not reformed.
^ Frequently thought of being the rationale of the Sunflower Official, the Queen Anne's Lace, and the Marquis de Sod, in that order.
*Please don't actually use dead baby jokes.
°If your counterpoint that random humor is funny is Monty Python or Invader Zim, please hold off. Monty Python is not 'random' humor, but a form of surrealism. Surrealism's base is from the unexpected happening or things showing a disconnect from actual reality. In Invader Zim, Gir spouting off all that stuff isn't showing him as being funny, but to show that he's stupid. The characters that are shown to be mostly intelligent do not find Gir funny.
++ The ability to be serious is as important as having a sense of humor. The ability to be serious shows the understanding that certain things need to be handled with more than a laugh.
^^ Characters with tales of dark, terrible woe are often Sues or Stus.