Back to the main story. This Academy Yu is attending is populated with students who also possess abilities, which you'll know the reason for soon after starting the anime, giving the story greater depth. The reason why they're all there is to protect them from scientists should they discover they have these abilities, for they treat them like guinea pigs and see if they can somehow use their abilities for other things.
These abilities bring in the comedy part to Charlotte. As Yu puts it, they're imperfect abilities in that at first they seem to be useful until we're told of the flaws, like being invisible but only to one person. The cool thing is that they're not standard abilities we know of; they're ones we wouldn't think of unless we're very creative (I guess). But even though the flaws make standard ones such as invisibility unique.
So how do the story and abilities mix in? Well, Yu is made part of the student council which currently consists of the couple who sought him out in the first place, known as Nao and Takajo. It's no ordinary council as they seek out other people with abilities to bring them into the Academy to protect them from others. They're located with the help of another member of the council who is just plain weird (you'll see what I mean). Yu's ability is deemed useful by them in that he can use it to stall people and make it easier to locate the person with the ability and convince them to come to the Academy. Although this may seem like it's repetitive as Yu and co locate these people, the new additions to the school council add extra comedy and depth in each episode. The characters' ability/abilities are not forgotten as you can clearly see throughout, making for some great moments amongst the drama.
With lots of abilities, personalities and pizza sauce, Charlotte has a good story in a world where special abilities are taken for granted by the user and those around them. Packed with fun moments and drama, the repetitiveness is disguised by the inclusion of new characters and comedy so you won't feel like it's dragging on.
A Lelouch look-alike is sought after due to his supernatural ability, and joins a school where he helps to find others just like him to protect them from those who wish to research their abilities for other things
Anything else: Otosaka special pizza sauce overload!