I had a similar situation in a recent game session. The difference was: i was the PC!
I'm playing a Duskblade, trained both in martial and magical stuff. Average Knowledge skills, which allow for that "who is this guy?" check, along with the "Collector of Stories" skill trick. On the other hand, his WIS sucks!
These are completely different skills, i know, but wouldn't it be logical for an experienced fighter/caster to be able to assess threats using the intellect and experience, rather than gut feeling?
My point is: i always see WIS as a skill for immediate stuff like Spot checks, Will saves, assess NPC reactions to the words you've just spoke, etc. Things that take (a bit) longer usually require analysis and a thinking process: Search, Appraise, Decipher Script...
IMHO, i could probably go with a houserule for this, that allowed for a Sense Motive check, yes (after all, you're "reading" a creature), but using INT as modifier and adding, say, 1/2 the CL to account for the experience...?