I'm reminded of one of my players, Bob, who played what was essentially a half-troll character for a time. With good players, these issues work themselves out. Bob's character had abyssmal PR and RE as well as IN. He embraced his inner troll, and made it a good time for everyone. Anytime a roll came up regarding social interaction, Bob would make sure all involved knew he was distractedly picking flesh out of his teeth with a blood-stained dagger, or bits of scalp out of his armor. When perception checks were solicited, we would turn to Bob, and say, "Are you going to make a roll?" - he'd smile and say, "Why would I? Did something edible just move?"
I think that ultimately, a discussion like that would be beneficial - encourage the player to embrace his limitations in a way that everyone enjoys. Make sure he understands that by making certain paper choices, he is making personality choices as well. If it's entertaining enough, it will become second nature. Then, you might let them get away with something that might be strictly outside their abilities once in a while, because of the RP value they bring to the table otherwise.
I also believe that given the hazards of the game environment, certain areas of expertise shouldn't be open to getting abused. Thak the Unimpressive might have no idea how to appraise fruits and veggies, or many common goods, but because fighting is his life, he knows how to evaluate a blade - insofar as it applies to his exposure. He might not know high steel from low steel, but he can certainly determine balance, heft, strength, etc. He might be taken on a "shiny" purchase, but the shiny would be functional, at least.