Wait so did aki end up with ayaka?
No, no one end up with anyone. Aki only work as his secretary for a while, cause it says she took temporary leave from school.
However, i think there's a God chance they Will.
Throughout the manga, between the original founder aki is seen interacting with akaya the most. Not that there's a lot interaction between two of them, but almost everytime akaya is there, aki also be there. Also if you read the prequel (Maken Ki! Kai!), there's a fair amount of ship tease between the two of them.
At the end of the day, it's a open ending, no one end up with anyone, a total waste of time, but maybe for the best. Takeda doesn't cut out to make a decent manga to begin with Imo, he's should've just stuck on hentai. But if there's a pairing that had a good chance of happening, i bet this two Will.