There seems to have been a massive code overhaul for Ruby and Sapphire that they've built upon to this day. Those old Key Items are still kept in the code. I definitely think another overhaul is long overdue, and it kind of surprises me they didn't use the occasion of Dexit to do so.
A counterpoint is that this playstyle isn't necessarily very intuitive. As a kid, I certainly didn't have a habit of rotating my team that much. What I caught was what I used, and that's generally a tendency I see from other players as well. Upon capturing a Pokémon you're asked to give it a nickname, which encourages bonding with the Pokémon. NPCs are always talking about your Pokémon as your friends and partners, which really discourages sending them to the PC. You wouldn't want little Lucky to miss out on that next big battle, would you?
The prospect of evolution and the potential of learning new moves by level-up also entices you to keep your Pokémon around, because you'll never know if it will evolve or get a move that makes it really good. The Pokédex can give you a small pointer of whether the Pokémon has an evolution or not, but it's still hard to tell whether a poorly performing Pokémon is going through a rough patch or if it has reached its full potential and simply is that poor. Without looking it up, it's hard to determine if a Pokémon is worth keeping, but many players might keep it "just in case it becomes good later".
There's also the tendency of recurring NPCs to keep the same Pokémon around throughout most of the game. Early on, Blue eventually discarded his Raticate, but the other team members remain the same from the moment he catches them until the Champion battle. Silver never discarded any of his Pokémon, nor did May/Brendan, Barry, Cheren, Hugh, Hau or Gladion. At one point, Calem/Serena discard a Fletchling they have at the very start of the game, otherwise their teams are static. Only N and Hop make significant changes to their teams throughout the game. I think that if the game is designed around a rotating team, it should have been a little more upfront about it. Talking more about reorganizing your team, NPCs explicitly referring to Pokémon being boxed, stuff like that. Perhaps gift Pokémon are meant to be subtle encouragements to make changes to your team (not-so-subtle in the case of the cover legendary in XY!), but at least for me, I tend to box the gift Pokémon if I've already built a team I'm happy with.
Then again, these days I tend to run two teams in my playthroughs, swapping between them after each milestone battle, but otherwise playing the games completely straight. It's surprisingly fun, and quite challenging at times.
Overall, I think it's easy to sell to players the idea of trying out new Pokémon, but there's some psychological threshold to overcome for a player to discard a trusted team member. I think the games could benefit from addressing that bit a little better.
