Bring The Ruckus!
The easiest way to get Moltres is to fast travel to the gate of the Isle, walk to the place where the bike lady is, and wait.Just started the Legendary birds quest and caught Zapdos. Named it 'Meep, Meep'. Working on catching the others next.
I HATE Moltres. It's such a pain to go after. It's that much worse than the old wandering Pokemon, since it can go over water too. Just missed it in an area, due to me not paying attention for a second or so.
Moltres comes to you.