I've thought about it a bit, and I believe that the reason why fanservice in Pokémon games annoys me is because considering the nature of the franchise, fanservice is
a fundamentally flawed idea. One of the most important parts of Pokémon is that everyone has their favorite-- whether that be the vicious Haxorus or the more tame Corsola. Imagine how thrilled Mawile lovers were when its Mega Evolution was released.
One might argue that since the Pokémon that got fanservice are, by definition, more popular, then GF would be doing a good thing in powering them up a bit. The problem with this idea is that it just attracts more people to the Pokémon, while the others sit aside, neglected. Imagine a world where only the really popular Pokémon-- pseudo-legendaries (to some degree), Lucario, Zoroark, Greninja, Pikachu, and so on got buffs that put them on pedestals far above their brethren. Pokémon fans would be divided into two groups:
- The group consisting of mostly younger players that just pays attention to the new stuff.
- The people whose favorite Pokémon didn't happen to make its way to the top, and deeply resent the ones that did.
This first group is Pokémon's main audience, but the second one might actually be bigger (as an example, a Google search for any Pokémon will yield impressive art featuring it [just make sure you turn on SafeSearch as you do it]).
Pokémon thrives on popularity, but to continue succeeding, it needs to remain balanced as well. Some Megas for less popular Pokémon did this well by shifting the spotlight away from Pikachu. However, when certain Pokémon spiral out of control, then not only does it really annoy us, but it's bad for the franchise too-- you can only sell so many Lucario figures, and when people get bored of them, Mega Lucario will only help a little bit, even as Spiritomb and Luxray sit to the side, deemed "unpopular". Little kids are a fickle audience, and they'd rather see something brand new than a "new and improved" Lucario design.
I'm no Codraroll-- as you can see, this is quite a messy post-- but I hope I got my message across. Thanks for reading!