I think they wanted you to appreciate first stage mons more, and for one or two of your friends, but not everyone to get the phone call that would give you the stone, so that it seemed more exciting. IIRC one of the original design ideas for Pokemon was an RPG that let you trade items among friends so that everyone has a slightly different experience. I think this was them trying to realize that idea. The games aren't hard, you don't need a team of fully evolved mons, and it's expected for you to take it slow. I beat Crystal with a Poliwhirl on the team, and he did fine.
As for the Johto pokemon, it's a bad move in execution, but I think they wanted both halves of the game to have exciting new mons, and I think that's as far as they thought.
A lot of people that complain about Johto seem to want the game to be a single-player battle simulator, whereas the devs clearly intended a slower, more social game that you play bit by bit.