I heard from someone who is trying to counter Saphira with a Mega Altaria, which could be a bad a idea because not only Naganadel, but Dragalge, which is kinda Sp.Def bulky, and its types. As for its ace pokemon. I'm surely it will be Dragonite, but I thought the same way with Hardy, which is not Gigalith, it is Lycanroc. If it is that way, then I'll goo with Salamance be her ace, allowing to mega evolve. As for format, pretty sure it would be Doubles, or, before battle, Saphira allows to choose (Like Amaria did).
Personally, if I would counter Naganadel, it would be with Assault Vest Tyranitar, pretty sure it can take at least 2 shots. And of course, planning to outspeed with Tailwind, and finish with Mega Charizard X and Naganadel.