I've said before and I'll say it again - Marcus has only a small role at the beginning of Raiders. Ignoring the ending, he's in it for three short scenes. Apart from him giving Indy some sage advice and introducing him to the Army Intelligence men, he doesn't have much of a role in the plot. I think Marcus' traits as a wise mentor to Indy are overstated, exaggerated and embellished by the critics of his behavior in LC.
Keep in mind also that for his first few scenes in LC, he behaves no differently than he did in Raiders. It's only once he gets to Iskenderun that he starts behaving differently than what viewers had seen up then. Even in Venice, he doesn't say or do anything that makes him seem incompetent or inexperienced.
Why then difference in behavior between Venice and Iskenderun? I think it's the absence of Indy. Marcus is an intelligent but inexperienced man (note his line "A few years ago I would've gone after it myself" is not evidence he's had field experience). At Indy's side in Venice, he can still function much as he does within the confines of academe, confident, self-assured, even a little impatient and snarky, but it's once he is forced to go it alone in Iskenderun without his old friend's son, that he shows signs of insecurity and confusion, not due to stupidity, but due to intimidation - notice he regains some of his old self once he meets up with Sallah. Now with a friend, a taste of the familiar, he is able to relax and carry himself normally, even becoming a little bit too sure of himself and let the Nazi agent sweet talk him.
Then when trouble arises, he is back to being confused and afraid, and while in Donovan's custody he is alone and afraid, apart from some defiance ("I'd rather spit it in your face.").
This just leaves Indy's jab about him getting lost in his own museum. I'm sure this happened, but Marcus sometimes seems a little "floaty" (in the sense that his self-confidence means he lets stuff roll off of him) so when it did happen I'm sure he didn't notice or care that it had. All this points to Marcus being a man who functions best in surroundings and situations that are familiar to him, to the point of walking between the raindrops and being a little inattentive but otherwise confident and self-assured, and who is easily intimidated by unfamiliar ones if he doesn't have a friend with him.
In other words, your average stereotypical middle-aged academic type.