Well let me phrase myself better: I don't get why games choose this design in first place.
As I said Pokemon is the obvious one, but there's been others over the years that do it (latest I can think of being Returnal where if you want to start over you have to delete the save data) and same applies, "but why".
I have a hard time thinking why a game should purposely negate to allow the player to have multiple save files. Moreso in modern age, while for very old hardware like GameBoy you could have made a point about cart space, it definitely doesnt work out for modern ones.
It's pretty simple: $$$.
Or, well, ¥¥¥ I suppose. The game is all about collecting, and bonding with your collection. I've always held that the "meat" of the Pokémon games is the adventure you're having, from humble beginnings in a small town to becoming the national champion with a full Pokédex and dozens of trusty monsters on your side. This experience of growth and progression is what really drives the games ... and if you want to re-experience it after finishing it, you have to start over. This involves
losing your entire collection permanently. Not only your Pokémon, but also your completed sidequests, item collection (TMs, Mega Stones, Berries …), your Pokédex, all gone. Some of it can be saved by trading (which requires you to buy another copy ... and maybe even
another console), but most of it would be irreversibly lost by starting over. That is, of course, unless you buy a new cartridge.
By restricting things to one save per cartridge, players need to buy multiple cartridges to play the game again, or face the loss of everything they've worked for. The games are cleverly designed (possibly not intentionally, but that's the effect of it) to give you great attachment to your collection, but also enticing you to play again. There are three starters to choose between, for instance. How would it feel to play the game with another choice? To find out, you must sacrifice everything ... or fork over a few more dollars, er, yen. Look, there's even a paired version you could try instead.
Also consider the situation of siblings playing the game. One save per cartridge means each sibling would need to have their own copy. Maybe even their own console, since so much of the game is about playing together. You need multiple cartridges cooperating to complete your collection, after all.
The one-save-per-cartridge model is a
massive sales driver. Just like the two-versions model. It's not friendly to players, it arguably doesn't make the game any better, but TPC rakes in So. Much. Cash. because of it.
Come to think of it, I wonder how well Pokémon would fare on the bestselling games lists if one corrected for the factor of people buying multiple copies of what is essentially the same game. They would still be massively popular, of course, but they'd be knocked down a few spots on the lists, I think.