(This begs the question of why skills and abilities need to be separate at all, but that's a bigger question for another time.)
D&D really suffers in this regard. Perception can't have a stand-alone score because there's no spot for it on the character sheet. So what do you tie it to? Wisdom is the traditional choice, but only because it's the least bad option. Wisdom has the unfortunate consequence of making clerics the best scouts. I don't know about you, but that really breaks the archetype for me. I have nothing against clerics; they're some of my favorite characters. But the cleric shouldn't be your go-to guy when someone needs to peek through a keyhole or find a gem stashed in a merchant's mattress. It doesn't make sense from a story angle or a game angle to let the cleric poach in the rogue's forest that way. It was bad enough when the cleric had the find traps spell.
There are four solutions that I can see.
Option 1 is to add Perception as the seventh ability score. I doubt that anyone sees this happening. The six ability scores are enshrined in marble, whether or not they make sense or serve the game. I appreciate as much as anyone why it can't happen.
Option 2 is step backward to earlier editions that didn't rely on skill rolls. It's true; characters used to perceive things without rolling dice. Finding things like secret doors was more a matter of time than observational skill. If you spent the necessary 10 minutes peering at, poking, tapping, and twisting every inch of a 10-foot wall section, you'd find the secret door. If the DM described a few features and you hit on the idea of pressing the gargoyle's left eye, you might find the door right away and save yourself considerable time and risk from wandering monster rolls. This removes a bit of p'zazz from certain character archetypes; playing the eagle-eyed detective who spots things everyone else misses is fun.
Option 3 is to decouple perception from Wisdom and let it float among the ability scores. There are plenty of occasions where perception depends more on Dexterity than on Wisdom, such as when you're groping along the top shelf of a bookcase in search of the hidden door latch. If the feature that needs noticing is the sort of thing that a sly person would be tuned into, then the roll can be based on Dexterity. If it's the sort of thing that a warrior would be tuned into, then it can be based on Strength. If it's the sort of thing that a wizard would be tuned into, then it can be based on Intelligence. No, this doesn't make a heap of sense, but it would work better 'round the table than always tying Perception to Wisdom.
Option 4 is to eliminate Perception as a skill. Drive an ice pick into it. When some sort of perception is called for, use the skill that most closely relates to the situation. Here are some examples, in 4th Edition wrapping.
- Finding a secret door? Thievery or Dungeoneering.
- Tracking a monster to its lair? Nature.
- Spotting the lich's phylactery? Arcana.
- Picking out your contact among all the bar's patrons? Streetwise.
- Noticing the fang marks on the corpse's wrist? Heal.
- Hearing someone sneaking up on you? Stealth.
- Spotting the demonic cult tattoo on an assailant's arm? Religion.
I'd love to see D&D Next take this direction. It's not headed that way right now, but we can lobby.