I sincerely believe that the only reason Fluttershy is getting a brother...

[LordofDiscord 2]

I don't think she hates him she just finds him annoying Zephyr is probably like this due to high expectations as a colt but the expectation killed his confidence and basically making him reliant on other people not helped by his shy parents Fluttershy Is probably the reason he knows his limits 

[EpicEnergy 22,153]

I think that the reason the writers brought in Fluttershy's brother is because they wanted to build Fluttershy's family rather than because they ran out of ideas for Fluttershy's character arc. Introducing a brother for Fluttershy gave her parents and herself more opportunities for interactions and character development.

[LordofDiscord 2]

Yeah she barely had any family before