One argument in favor is niche protection. If you have to have two skills to be able to perceive enemies then all characters won't be just good at that. In 5e, almost everybody who can takes Perception as a background skill. So most characters are good at noticing enemies. In 3.5, especially with cross class skills a lot of times it's not worth it to do that on a character that doesn't have the skills or the points. So you get a system where a person who is specialized in those things is rarer and more rewarded for that. It's one of the things I disliked about Pathfinder's skill thing, by making all the skills cost the same you basically deal a pretty big blow to the classes who are specialized in those things.