My thought is that if this is supposed to be a C rank to replace or reinforce Wave arc, then it should be chosen based on how you want it to affect Naruto and his relationships with other characters.
Here are some ideas partitioned into categories for your benefit.
Standard: missions that are pretty typical of what we've seen and what might be expected of Team Kakashi. That does not mean that the mission will play out in a "typical way" of course.
Guarding:
A merchant caravan running along usual trade routes requests a ninja escort. These are pros who trade their wares in many countries and are used to hiring ninjas. It's a large caravan with only a gennin team covering it so unlike Tazuna they will not doubt what these kids can do. Shit hits the fan when it turns out one of the merchants might be carrying something that somebody else might want. Perhaps Naruto's team faces a team from another village like Iwa or Kumo. Exactly how you build the complications should depend on what you want to get out of it. For example, Naruto could meet another jinchuuriki a little early. Or maybe it's something more simple. Maybe he's forced to make his first kill and it really rattles him.
Investigation:
Some people from a certain village have gone missing. There's no particular reason to suspect foul play is involved, but the villagers hire Konoha ninja hoping to get to the bottom of this anyway. Again, many ways in which this mission could get complicated and many possible things Naruto could learn. This type of mission is well suited to Team Kakashi as well since Kakashi himself is supposedly very smart, has the Sharingan and has his nin dogs, Sakura is supposedly very smart, and Sasuke is supposedly smart, comes from a family of military police and has his Sharingan. Naruto is actually the odd man out. In this situation his role would be to provide support. This makes this choice somewhat more interesting than the first (where Naruto would actually be the most effective of the three gennin due to Kage Bunshin allowing him to help the caravan and fight simultaneously) in that it highlights Naruto's shortcomings. Unless of course you are deliberately writing some kind of genius!Naruto.
Investigation2:
A building that is supposed to be abandoned (such as an old fort) suddenly is showing signs of habitation. Naruto and his team are sent to investigate in what is expected to be a routine mission chasing out hobos or bandits. Instead they wind up in way over their heads.
Investigation3:
Naruto's team is responsible for investigating a particular person or organization. This type of mission would be okay for Team Kakashi or Team Asuma in canon, but Team Kurenai and Team Gai are not as well suited for it, particularly Team Gai. The other three missions above can really be done independent of your choice for Naruto's team. This type of mission is probably routine for Konoha and someone like Kakashi might accept it as an opportunity to train his students. Unfortunately, this background check does not go so well as they discover things that should have been kept buried.
Political: another option is to create a mission with a political bend to it. We can talk about this from the POV of foreign relations (which can always play a role in any Naruto story), or we can talk about this in terms of court politics, which is sometimes irrelevant (in canon, for example).
For foreign relations, any of the previous missions can be tailored to include a fight with ninja from a foreign village and perhaps even real consequences. Maybe Naruto kills someone important and this causes a war to start. Maybe someone from Konoha gets killed off -- Naruto's sensei or a teammate. The fact that Naruto is a jinchuuriki may suddenly become common knowledge abroad, if it wasn't before, influencing how the Sandaime uses Naruto. This can in turn lead to court politics, if you let it.
Yukie:
If you're looking for a politically oriented mission, one option is to redo the Princess Yukie mission, except instead of doing a copy/paste of the movie's plot, attempt to do it realistically. No mystical seven colored chakra that instantaneously changes the country from winter to spring. Probably no movie or anything like that (the movie within a movie was silly -- it worked surprisingly well, but it was silly). Naruto ends up playing hero and saves the princess. If he's canonish, this probably inflates Naruto's ego a bit. Not to the point of douchebaggery, but certainly more than it should. Meanwhile it involves him in a major political incident.
Noble Evil:
Naruto and his team are sent to deal with a local disturbance, but find that the root of the issue is political in nature, with an obstructive bureaucrat or a local feudal lord who is outright despicable impeding them for what almost seems like no reason.
Unusual: a couple unusual ideas I've had.
Jiraiya:
Naruto and company are given a mission who ultimate benefactor is Jiraiya. He's giving Naruto this mission as a way of doing something without doing anything. This can even be before Naruto and Jiraiya have met. It's supposed to be a routine mission, but as you may expect by now, shit hits the fan. The mission itself could be something like a routine background check, or transporting ten thousand copies of Icha Icha. The result is the interesting part, with Jiraiya being involved unexpectedly. I'd recommend making Jiraiya's involvement unexpected for the audience as well as Naruto, so that when he does show up it comes as a genuine surprise.
Police Work:
Naruto and company are hired to work as security at a major festival. This can be played straight or for crack.
Final: one last comment is that you do not need to give Naruto a C-rank. You can always give him a D-rank the morphs into something beyond his pay grade. For example, Naruto's team may be asked to deliver a message to outside the village. It's not sensitive material, just routine mail or supplies that requires promptness.
Ultimately, it's the complication that hits the mission that will determine how effective the mission is at telling story.
Also, be careful not to fall into the trap of mislabeled a B-rank mission as C-rank. For a list of known mission ranks:
<a href='http://leafninja.com/mission.php' target='_blank' rel='nofollow'>http://leafninja.com/mission.php</a>
Anything that potentially involves running across foreign ninjas, such as infiltration, escort against potential ninja threats, etc., would be B-rank or higher. A mission that definitively involves combat against hostile bandits would also be B-rank or higher. C-rank escort is for protection against the possibility of bandits, not for eliminating bandits outright. Such a mission would not normally be given to gennin.