My frustration is mostly that it happens all the bloody time in so many series.
I feel like it's probably just a cultural thing for the Japanese writers. Most writers seem to just not like tomboys. If there's a harem they're the losing childhood friend because they can be nice but the audience won't feel too bad if they lose because they're not a proper girly-girl like the FMC. If there's no harem and they are the winning heroine, it usually comes with the relationship causing them to embrace their girly side and cast away the tomboy trappings (short hair, athletic background, liking boyish things or not dressing too girly) so that she can be a "proper" girlfriend.
It's sad because tomboys are plenty feminine if they just get to be themselves.