Yeah, I'm pretty sure it was planned from the start. How refined the idea was is another story. Shanks intimidating the Sea King with his glance was already the first hint. Then came the introduction of Logia through Smoker in chapter 97 and I'm sure Oda at that moment didn't consider Logias to be only beatable by some very specific weaknesses. Did he really think at chapter 97 that the pirate king Gol D. Roger could've beaten Smoker only by coming up with some specific counter to Smoke, or later to fire, sand and lightning? With Zoro cutting through Daz Bones and the Priests and Enel using Mantra, at this point Oda was making use of that concrete idea already.