I had to think about this a little but I'd say that Houndoom is a prime example for this.

Despite her ace Pokémon being Talonflame, Houndoom was actually her very first Pokémon that she got when she was a teenager. They've been together for a long time, and he was the only one who witnessed Briar's situation at home so he was always naturally protective of her. In Team Flare too, since when you're part of an organization like that, you need the extra security at all times.

But the real sense of protection came after Team Flare was disbanded and Briar fell into a deep depression. Houndoom, who had been there since the beginning, promised to never let Briar go that low ever again.

They've been together for years, decades even, so their bond is quite strong, and this is exemplified by the fact that it is Briar's only Pokémon capable of Mega Evolving, which happens when you have a strong bond with your trainer. Houndoom's desire to protect Briar is so strong that he would gladly go through something as painful as Mega Evolution if it gave him the means to keep her safe. And he is the only Pokémon that she has that can do something like that—go that far, for her. This doesn't mean that her other Pokémon don't care—they do, they love her a lot—, but none of them have been there since the beginning like Houndoom.