>>45648087At least in Gen 4 they justified it by having a lot of the new babymons show up in earlier routes. Having Roselia pop up on one of the first routes would have been a bit unbalanced, plus introducing a new babymon early-on gives players that otherwise wouldn't have wanted to use Roselia a good reason to pick one up, which also further exposes the player to the newly added Roserade.
Gen 3 didn't have a good reason though. Not only was Azurill unobtainable in the wild, but Marill was slapped onto one of the first routes. Wynaut at least almost justifies it's existence, giving Wobbuffet access to more than four moves, as well as working well as a gift Pokémon, but sticks out like a sore thumb when Azurill is the only other baby in the gen. And if they wanted to give Wobbuffet new moves they also could have just expanded it's learnset or added egg moves.