There's the aforementioned eidolon store in the kind-of-distant future to help max out spare eidolons. Not that you would, but still, it's there.

In the more-distant future (December), there's a shop for raid ssr weapons. The currency needed for that is generally preferred for a different endgame usage, but it's an option, especially if you're not far away from maxing out the spare in question. Said currency is obtained as rewards for completing X weekly missions in hardest-content-at-the-time, Guild Orders (introduced in August). Once introduced, Guild Orders will always be there, rotating through elements.