Perception skills are going to be very situational.
Recon is a good "general awareness and paranoia" case, but I'd ask for a roll on Engineering if the thing I was checking for was related to engine room conditions (like imparting to the group's engineer that there are way too many red-lined indicators on that powerplant), or a Carousing, Recruiting, or related roll to determine that a person I was speaking to was nervous about something. Investigation is the "Search a room" special case, while Medical might be the skill to check for detecting an alien in disguise (per "The Trouble with Tribbles").