I'd support new ways to skill up, but I wouldn't support the idea of using merits to do so. The reason is because, as you say, it's simply too easy to cap merits these days. People would find themselves entirely neglecting their skills in favor of rushing to level 90 and capping them with merits instead.

Perhaps a system whereupon players could expend merits for a boost during combat, similar to how Atma's give players a boost in Abyssea except these boots would work outside. Perhaps new powerful skills could be added which spend merits as a form of currency to perform. Such things would probably be very useful against powerful NMs.

Just my thoughts on the matter, but I certainly agree that we could find some unique uses for the merit system if we think outside of the box.