The simple solution: Game Freak doesn't care in the slightest. Sure, they care that the majority of Pokemon should have decent enough stats when they reach their final evolved form, and that Legendaries should be more powerful than Bidoof, but in the end, if Game Freak doesn't think this specific Pokemon should get a good speed stat, it's not going to get one.
A perfect example of this is Flareon: People still cry out that it, with a 130 base Attack, should have access to Flare Blitz, but it doesn't. The reason why Game Freak never gave Flareon Flare Blitz: They just didn't think it should get it. Not cruel malice towards the poor Eeveelution, not absurd levels of laziness, it's just that they don't really think Flare Blitz belongs on Flareon as a Pokemon species, instead of looking at Flareon as a competitive weapon and giving it Flare Blitz to make it better.
Game Freak doesn't think competitively. They didn't realize the clever ways Wobbuffet, a Pokemon that wasn't really supposed to stand out all that much, could be used, and as such we get a lethal joke character that got kicked up to Ubers. Similarly, they made Black and White Kyurem without making them stupidly competitively viable, and because of this it's only in OU instead of Ubers due to its typing, despite it's BST.
In short, Game Freak makes terrible Pokemon because they don't really care how good it is in the first place.