Yeah, the difference between Perception and Investigation is kinda confusing. If it helps, keep in mind that animals can have a very good Perception bonus but rarely are good at Investigation. That's because Perception is more about how good your senses are; it makes you aware of things. Investigation is about how well you process what you perceive; it makes you recognize things. Investigation has intent. You always know what you're trying to find.
The problem I have with it is the concept of just using "investigation" on something is really nebulous. All the other Intelligence skills are based around knowledge about a particular topic. What sort of knowledge does Investigation use? The knowledge of... what clues mean? ...how to find clues? These all seem like things that would be better-suited to a specific knowledge check. I'd rather replace it with another one of those, maybe 3.5e's Architecture & Engineering check. Then you could break it down like this:
Arcana: Finding magical lore, identifying a magical device or effect based on clues
Architecture & Engineering: Finding hidden doors, identifying man-made traps, locating a structure's weak point
History: Identifying what civilization an artifact came from, figuring out why something was created
Nature: Identifying natural hazards, deducing whether or not something is poisonous, investigating a dead person's cause of death or time of death
Religion: Identifying the god a temple was built for, working out what ritual was performed based on things left over
Generic Intelligence checks: Any other kind of investigation