Um, you mean that the special ability of the synchro form, a.k.a., Ash being able to share his vision with Greninja wasn't useful during the TF arc? That literally helped Ash to mark Chespie's location in the Megalith and in the process saving Chespie? Without marking Chespie's location properly, saving Chespie and saving the Megalith would've been impossible. It's clear that the syncrho form's special ability was the key there.
It was useful, but for how much the writers propped up the prophecy, I expected a more epic portrayal of Greninja being the prophesied hero.
And you can't really expect the boost from the synchro form to be higher than Mega Evolutions like Alain's Mega Charizard X. Because Mega Evolution boost depends on the strength of the bond between the trainer and the Pokemon, how much experience one has with Mega Evolution. Alain shared an unbreakably strong bond with his Charizard, had the goal of becoming the greatest Mega Evolution trainer, worked hard day and night for it, has enormous experience with Mega Evolution (pretty much used ME in every battle). So not getting a higher boost compared to Alain's Charizard is understandable. But still, compared to the other Mega Evolutions shown in XY(apart from the ones belonging to E4 members and Champions), it did provide a considerably higher boost.
That's exactly my point. They could have differentiated Synchro Evolution vs Mega Evolution with Ash/Greninja having a significantly more powerful boost than ME, but they have to work up to it each battle and they're unable to sustain it for any longer than X amount of seconds. That would be in contrast to Mega Evolution, in which trainers can use it right away and it stays until the duration of the battle, but doesn't have the crazy boost of Synchro Evolution.
As it stands now, Alain/Charizard also helped save the day, Alain didn't need to have any prophecy for his Charizard, and Alain could Mega Evolve his Charizard to an extremely powerful level without suffering from the pain-sharing mechanics of Synchro Evolution. Meanwhile, Synchro Evolution comes across a vague, power up that's essentially "Mega Greninja" all in but name.
^ That's just one idea too. I already talked above about how the pain-sharing mechanics or synchronous wordless communication could have been presented.