Starting off with a fun fact: Will's original concept was Ken Du, who was just as capable as Kim. They had a rivalry with each other, but also a bit of a romance. Concept art had him looking just like Hirotaka.
So, honestly, the idea of Kim having an actual rival in saving the world is so interesting. Unfortunately, Will doesn't measure up to Kim.
Or, he's not supposed to.
But he's the top agent at Global Justice for a reason, so there's probably more to his mistakes on the mission than being incompetent.
The first thing we learn about Will is that he doesn't want to work with an amateur. He finds it insulting that he's being asked.
Instead of it being snobbery or an insult to Kim's abilities, it could just as easily be that he wanted to get the job done without having to teach someone else to do it, and was insulted that they wanted to waste his time by making him teach someone to do the job.
I mean, I don't know how it works in the world of espionage, but in every job I had, if someone of high rank was being asked to work with a new recruit or potential recruit, it's because they were expected to teach them or determine if they'd be good for the job.
(Also, Kim needs to not take being called an amateur so personally. She never even fought an actual bad guy until "Tick-Tick-Tick", which was less than two months ago at this point. She is definitely skilled, but she is technically an amateur.)
And Kim is someone who said, to Dr. Director's face, that she's wrong about why someone would kidnap Professor Green because "you can learn everything he knows at the library."
(Honestly, odds are that wasn't true. This is the era where computers were still boxes, Wikileaks didn't exist yet, and only nerds spent a lot of time online anyways. There were still projects from WWII that were classified, so it's doubtful that everything Professor Green worked on was declassified.)
Will Du and Global Justice assume Professor Green had been kidnapped for his weapons knowledge. Even if that wasn't why he was kidnapped, they still have an interest in making sure none of his weapons knowledge got out anyways.
But Kim keeps insisting that the trained professionals who do this for a living are wrong.
It must be really frustrating for Will.
(Just because Kim was right doesn't mean she has to be a know-it-all.)
There's also the fact that Global Justice had only asked Kim on the mission, but she brought Ron and Rufus along anyways, meaning in addition to ensuring Kim's safety, Will also has to ensure the safety of a civilian and his pet, who should not have been there in the first place.
Despite Will having an entire database of verified information on his wrist, Kim insists on going to a den of criminal activity to talk to some crime boss for information, despite being unable to prove the information would be correct or helpful.
(And does not tell Will ahead of time where they're going, denying him any ability to refuse to go or offer an alternative.)
Sure, it got the job done, but Will no doubt has procedures, rules, and regulations to follow, along with a list of things that he shouldn't do, and using unverified, known-criminal sources for information is probably one of them.
Will has to ensure the safety of an amateur that charges into things without talking to others, and the civilian and rodent she dragged along who shouldn't be there.
Will has to follow rules and procedures that Kim doesn't think about and likely wouldn't respect anyways.
Will has a database of useful and verified information, but Kim insists on using sources like Big Daddy Brotherson.
Kim went into the mission with an "I know better" attitude, already believing she was better than the professionals who do this for a living.
So, while Will is probably actually extremely competent, he was also off of his game because his style doesn’t mesh well with Kim’s at all.
And he would have been an interesting recurring character, but the creators decided not to give Kim an actual rival in saving the world, for some reason, so we never see Will again.
(I like to imagine he specifically requested to never work with Kim again, so Global Justice only contacts Kim for things that Kim would be better suited for, or when they were studying The Ron Factor.)
So, Will could have been a very interesting character, someone to serve as an actual rival to Kim when it comes to saving the world.
Sadly, his potential was wasted by turning him into a seemingly incompetent agent.
And that's just sad.
Will doesn't seem to be very experienced with combat. I'm not saying that's a bad thing, it just leads me to a certain conclusion about him:
He wasn't trained for combat.
Global Justice's top agent would be very skilled at whatever they needed him to be good at, but combat doesn't seem to be one of his skills.
So it's very likely Global Justice probably didn't need him for combat. His skills probably lie more in intelligence gathering and espionage, which requires more stealth and diplomacy than fighting
And it certainly never involved fighting villains like Kim's.
Thus, Will is not incompetent, he's just not suited for combat against supervillains with gimmicks.