The bottom line is about more than just cash grabs. SE is in this for long-term profits, and for that they know that they need customer loyalty. You can bet that any item they put into the cash shop, INCLUDING skip potions, SE will carefully weigh just how much they can afford to annoy their playerbase. Ideally, sure, they'd love to nickel and dime us at every turn like a freemium game, but they know very well that such behavior would turn players away in droves, resulting in long-term profits that are MUCH lower than they would be if they kept that impulse at bay. As such, they're careful about what they put into the cash shop.
That said, I would be not be surprised to see skip potions available for free (at least, the first; additional skip potions to level other jobs might incur a charge), as a way to attract players to the game who might otherwise be turned off by the long main scenario grind to catch up to Stormblood. While SE has promised that some Stormblood content will be accessible without being caught up on the main scenario, you can bet that anything endgame will require it. For players who want to join FFXIV to participate in difficult endgame content but aren't interested in the story of the game, it could be just what the doctor ordered.
My biggest fear is that players who WANT to experience the story will feel pressured by other players to skip ahead. "What, you're level twelve? What are you bothering with all that crap for? Just skip, the story sucks anyway. Endgame is where the real fun is!" Only to discover once they get there that Endgame wasn't the paradise they'd been told. With no endgame, and no story, all that's left is grinding tomestones for gear in dungeons where the player has no idea why they're even in the dungeon. It's hard to imagine a player sticking around long under those conditions.
I hope that the potion comes with a pretty explicit warning that by using it, the player will be permanently lose the ability to read the whole story from the beginning, so no player is caught by surprise.