I never said anything about Zygarde doing more than Shaymin. Everyone needs to accept that. I don't really like Shaymin, but just like Zygarde prior to it, it felt like the writers handed legendaries to these girls just so they could look relevant. "Oh hey, look here! I am kidnapping this legendary here so I will actually feel relevant for once instead of being a female version of Max (!). Shaymin is a legendary, Zygarde is a legendary. Bonnie was a companion, Mallow is a companion. Shaymin not being relevant wasn't even my point.
Fair enough.
She became a bit sad when leaving Tyrantrum and Flabebé (though I don't think the Lapras goodbye was as emotional like these others since the cotd kids had more of a bond with it than Bonnie) but she bonded way more with Puni-chan than she did with Tyrantrum and Flabebé which were featured in filler episodes while Puni-chan was basically the key character for the entire TF arc. Of course her final scene with Puni-chan would be more emotional since she only bonded with these 3 Pokémon for a few minutes while Zygarde was under her care for the most part of XYZ. The problem with that is: this development was featured mainly in filler episodes because while it shows a tiny bit of development for Bonnie, you can skip it if you want and by the climax of the TF arc you won't even remember about it.
Which were, for the most part, fillers.
Being cute don't make a character interesting, y'know.
That's exactly the problem though. Somehow, if a bit of that focus went to Serena, her character would be much more enjoyable.
No, but you did pretty much say that Mallow and Shaymin's arc is the same as Bonnie and Zygarde's arc just because they both carry legendaries around, which is unreasonable, cuz the latter actually has a storyline and their bond do serve a greater purpose (also, Shaymin is not a legendary, but that is beyond the point).
If it has character development, then it's not that dispensable. You can chose to not watch it if you want to, but you shouldn't complain about not understanding the character later on, because that was your choice. Filler is a fan term that has two uses: one is to describe episodes that aren't part of the original source's canon (which is nearly the entire Pokémon anime) and the second is to describe episodes where either the plot or the main characters have no development (and you said it yourself that these episodes had development in it).
Also, if you payed enough attention to Bonnie's focused episodes, which you are so ready to dismiss, you would have seen that she wasn't useless. In these episodes, she was actually fighting and helping Pokémon. Even in episodes where she wasn't the focus, you could see her trying to help, like in XY061.
Handing all of Bonnie's development to Serena wouldn't have made much sense. These two character arcs had completely different themes and subjects. Serena's character was about self-discovery and gaining confidence, while Bonnie's character was about learning that you do not always get what you want and sometimes what you want is not necessarily what you or your friends need. The idea Bonnie's development was detrimental to Serena's is not reasonable at all. If they wanted to make more episodes focused on Serena, they could've without removing Bonnie's episodes.