It’s only doing that because this is an anime original. For Key’s other visual novels, we already know who’s gonna end up with who, and we get to see over 50+ hours of character development. For Charlotte, we know that Nao is gonna be the main heroine, but we only have 13 episodes for the love “character development” and of that “13 episodes” there has to be something to push in the thinking of them being a pair, mostly for people who have no knowledge of Key whatsoever. Plus, remember, this is the first Key anime/visual novel to have a girl that differs from the rest. (No spin-offs included). If it makes sense, Nao has a realistic personality compared to the other Key heroines. And Yu, he has a pretty much rude personality, yet he is also caring at the times he wants to be. It’s not surprising for Yu and Nao to be the end girl.
Also, I don’t think that the pairing is anything out of the ordinary, I mean, people didn’t like the (Little Busters spoiler) end girl for Little Busters. How Rin ended up being the end girl. Some people loved it since it was foreshadowed, mostly in Refrain for the general idea of the world, some people didn’t because of the pacing of the love.
As for Rewrite. (Rewrite spoiler) Kagari being the end girl, same thing, some people loved it, some people didn’t. Some people loved it because of the general concept of what Kagari was. Some people didn’t like it because of the pacing and the out of no where “I love you” ending, which, I didn’t really mind. It’s not the first time in Key where someone blurts that out of no where.