Ok, what
Have you no soul
Granted, there are some Pokemon that have been been lost to time, even in my old games.
But I definitely have Pokemon I'll never "let die," like my original team on Sapphire.
Do you ever think about dog breeding? Dog shows are followed by an entire network of breeders. Champion dogs die at some point, but the competitors still try to keep their fame as a top-notch dog breeder. In a lot of other games with multiple installments, you don't have the ability to move character data around. You have to build yourself back up from the beginning every time.
Pokémon, interestingly enough, gives you the opportunity to hold on to your favorite parts of former games. They separate the Pokémon continuity by creating an outlet to retain old memories and Pokedex slots. However, what matters about transferring is what is done with the Pokémon transferred. After the journey they were a part of, there isn't much to do with them that you couldn't do with new Pokémon during the main game. Each favorite that you move into a new game will probably:
a.) have to get its moves (and maybe EVs) reworked to be as useful as possible if you want to use it for post-game challenges
b.) provide support for exploring post-game routes
c.) sit in a box for you to look at every so often.
What starts as a travelling companion ends as a trophy. Your former teams that have won Pokémon leagues and ribbons start to build up shadow boxes in your PC. What's the point in keeping a landmark item like that if the most it can do is go in for wifi battles and fill a Pokedex entry?
To go back to the dog analogy, I think of my games as a continuing dog plantation with continually-improving graphics. New ones are obtained, bred, traded around, and eventually lost. But, the point of having a plantation is to always have dogs, even if your old favorites are gone. Having new dogs coming in is a means to stay busy raising dogs to meet their potential like what was done with their parents. I don't mind replicating that cycle in my games, because breeding children from my former champions is just my way of remembering their legacy.
Forgive me if I broke into any Kyubey-isms, but while I can see the competitive importance about having useful Pokémon with good specs, I don't see what's so great about any one person's Adamant-natured Swampert with maxed out Hp and Atk EVs.
But this isn't really the place to discuss the morals of training choices. Right now, I wanna know how high and low we have to search for Mega Stones. Will NPCs be holding them? Are they all hidden items that you need an Item Finder for? Could any of them be bought in specialty shops? Do we need Pokémon mounts to reach them? Are they found in special rooms or shrines dedicated to the Pokémon that the stone belongs to?