By now, with there being no major updates (as "extra data" or otherwise), Pokémon Shuffle on the 3DS is likely about to meet its demise along with the online services of the 3DS itself. Shuffle is still a great game regardless of what may be about to happen. Even so, it could still be an even greater game if a few of its features were to be revamped. Based on my most recent plays, I've identified a few of those features as well as what could be (or have been) done to improve them.
The "area browser" and the next/previous area buttons are good for basic navigation purposes, but they can stand to be more integrated. Specifically, the next/previous buttons could have options to navigate to stages instead, with the most viable options being to stages that have not been cleared, had its Pokémon captured, or received an S rank. The latter two is notably included for reference in the "area browser", so they constitute logical upgrades for the buttons. Better yet, they could be somehow be integrated to provide all of these conveniently, even with an "advanced navigation" feature. All of these could be improvements regardless.
Every stage demands the selection of Pokémon, and the Pokémon selector allows to do just that, especially with the help of the search filter options. However, with the advent of the Raise Max Level and Mega Speedup enhancements, it would be conceivably beneficial to filter Pokémon according to the condition of these two enhancements. For example, it could be helpful to search for Pokémon that have not been fully enhanced in order to enhance them, or the ones that are fully enhanced to be selected for battle. The addition of these filters would help to find those specific Pokémon instead of having to check each of them one by one, as I've sometimes had to do.
While some people love the Mega Evolution music, it seems rather frenzied for others, as I've noted once; I've known a few people who think it's grating in the latter case - even I've mostly played with music off recently. Therefore, a potential future request is a way to disable the Mega Evolution music in favor of a different auditory indicator for Mega Evolution, for example a constant buzzing over the normal stage music, which would indicate that Mega Evolution is active without being over-the-top in doing so, possibly leading to annoyance or frustration in doing so. Of course, for those who enjoy the music without any ill effects of any kind, they can still do so; the option would be simply and wholly optional for certain people.
It's been a great ride for Pokémon Shuffle since its launch, and it may be disconcerting that it along with 3DS online services are likely about to end soon, based on the current state of things. Before that happens, it may be wise to try to implement, as above, just a few additional improvements to its features somehow in order to improve the quality of the game even as its lifetime nears its end. In that way, people like me may just be able to enjoy the game for quite a bit more before it "shuffles" to a demise.
One year ago: The State of Nominations, Part 6
Two years ago: Standing Pikachu Keychain
Three years ago: The Merits of Sleep
Four years ago: Elite Four: "Courses" vs. "Selections"