The other simanim eaten on Rosh Hashana contain a play on words with the name of the food and either a wish for a good omen or a wish for bad to befall our enemies. The yehi ratzon for the apple has no such play on words. Why not? And then, why do we eat the apple at all (not mentioned in the gemarah in krisus).
We wish to have a sweet year. We symbolize this with sweet food: apples, honey. Thus, no pun is necessary.
A pun is necessary for, say, leek, since it lacks sweetness.
Dates would, I suppose, not need a pun, since they're sweet — but we can get a pun in, too, so we do.
Source: my own conjecture.
Since Apple in Honey is the only one of these Yehi-Ratzon that Chabad says, it must be unique, and presumably has a different reason/origin from the rest.