... a Magical Girl, a-la Sailor Moon, Card Captor Sakura, Magical Girl Lyrical Nanoha, or Puella Magi Madoka Magica...

Or a mage from Mahō Sensei Negima!...

Or one from any Final Fantasy continuum...

Or a Chi Wizard, like Uncle, from Jackie Chan Adeventures...

Or a Bender from Avatar: The Last Airbender and Legend of Korra...

Or a mage from Tamriel's Mage Guild or Skyrim's College of Winterhold from The Elder Scrolls...

...and there are all the options that can give you the Marvel and DC Universes...

In short, you have a lot of options from countless universes to choose from.

World One magic.

No, for serious, a stage magician kinda person would be an interesting agent, especially if their tricks somehow contrived to work. =]

I've seen lots and lots of that archetype since I read lots of fantasy. If you're willing to throw yourself headfirst into a new continuum, I'd recommend familiarising yourself with Dragonlance, then thinking about a Bozak Draconian - but only if you can be very careful, as the Bozaks' large amount of power requires careful management in order to avoid making your character a Sue or Stu.

The player characters basically draw power from one of eight elemental spirits in order to cast spells.

My favorite Let's Player helpfully provided a guide to the spells starting here, though he didn't know at the time what Evil Gate does (halves health).

In fact, I actually have an agent from this continuum: Chakkik. As a duplicate of the Mantis Ant, he's able to cast the most basic level of Gem Missile.

However, I did have one stipulation: Chakkik can only use magic in Square Enix continua. In any continuum that isn't Final Fantasy, Kingdom Hearts, Chrono Trigger, The World Ends with You or the Manaverse, Chakkik can't commune with Gnome (the earth elemental) to cast Gem Missile.

Of those three, I think that the Dresden Files one would be good. It's very expansive and has a lot of different niches for a character to fit in while still being well-defined and limited in a way that wouldn't make your characters Sueish.

However, it does tend to mess with technology, so a Dresden Files wizard would probably need special accommodations built into all their tech, and that's something that would need to be considered.

It's a pretty good webcomic (the it-gets-better-with-time kind) with an interesting system for magic. It's easy to mess up, though, so, if you're not familiar with it, I'd recommend Dresdenverse.

My main advice is to pick a continuum you know really well. Magic rules are frequently complex, and a poor grasp on them (especially their limitations) can make a character come off as Sueish, or just poorly developed. Another thing to keep in mind is that unless they're doing a mission in their home continuum, your character probably won't be able to access their powers. This can make for some interesting characterization moments.

I can't really comment on the other two you mentioned, but if you want a Dresdenverse wizard, I'd recommend checking out the RPG. It's got a lot of good setting information, as well as rules for creating a balanced character. Remember, the majority of magic-users in the setting aren't good enough to qualify as wizards; if you don't want to get into the techbane aspects, lesser talents generally don't have them so much. Also, don't just make your character a Harry clone (unless, of course, that's literally what he is!).

Other continuums to look at:

RPGs in general are a good choice because they typically feature a large range of options. Pathfinder, in particular has some interesting variants that could make for a good agent - I can see a lot of interaction between a Haunted Oracle and the Laws of Narrative Comedy, for instance. Either Mage: the Ascension or Mage: the Awakening has some interesting thematic parallels with the PPC, but remember, their partner will probably count as a Sleeper.

Personally, I'm a Fate/Stay Night fan, and a Nasuverse magus would be an interesting character, but the setting in general tends to be very complicated. I'd only go for it if you feel very comfortable with it, but if you are, it'd be a good choice. Or maybe I just think Waver would make a good agent...

I think you might be thinking about this in the wrong order. It seems like you're looking at the combat effectiveness of your agents first, rather than who they actually are. You'll have a much more well-rounded character if you figure out who they are and what they stand for before thinking about how they'll fare against a Sue. Remember, agents typically aren't warriors; they're normal people put into abnormal conditions and given a difficult task.