Well, I've always thought having Pokemon evolve by leveling up at certain locations added more depth to the game world. The same goes for Eevee requiring at least two levels of affection to evolve into Sylveon. In fact, I thought there should have been a few more Pokemon requiring raised Affection and leveling up near Moss/Ice Rocks and special magnetic field to evolve, actually.
As for Incense breeding, I also think this adds more depth to the games, and Baby pokemon often have poor stats and movepools, so they aren't always fun to raise.