I do feel that Pokémon would benefit from a stronger narrative. In general, Pokémon feels like it's too afraid to break through the norm and try and experiment with different things as most of the games since its conception, it hasn't broken out of its confort zone. For instance, you still do have archaic elements like the HMs, which have been toned down in recent years (ignoring ORAS for some reason), but it hasn't fully evolved from its old practice because that was how it done since the beginning. The narrative is in a similar place as we've been going through the motions for years, but aside from Gen V, it hasn't really tried to do other things with itself. With XY in particular, you went through the same basic progression: go get the badges, go beat the team, get your legendary, beat the league and Champion, all while fighting your rival(s) along the way, yet all of those elements felt lacking and got a lot of criticism. There are many complaints that have the Champion be seen as forgettable, the rivals being mostly disliked for not taking advantage of their goals, the legendaries popping out of nowhere with little depth, and Team Flare having bland roles until the plot tries to force a mature element that doesn't fit. In a lot of ways, by playing safe, I felt the games shown how stale things were getting with the typical formula and ended up feeling stagnant in a lot of ways.
Really, there's much that they could do to improve from those elements and evolve into something better, even if it doesn't mean fully dropping the league aspect. BW shown that they can have a stronger narrative in the games with a similar formula, so maybe they can use that as a building block and try to experiment more with what can be changed to further the games without fully losing its foundation. Experimenting can be risky but with a franchise that has just reached its 20th anniversary and has been criticized for its lack of evolution over the years, it may be time to take those risks. See what works, see what doesn't, they're not going to know unless they don't try, and Pokémon is at a point where poking for ways to get out of its box may be worthwhile.