What Jimmy can and can't do is total speculation. We have never seen him operate a real pro offense.
It is quite obvious he lacks the ability to push the ball down the field with consistency. That is why he never tried it. He has a weak arm. That was known at Notre Dame when he threw floaters to Floyd and Tate but it wasn't brought up as much because they bailed him out. His limited skillset is why he fell to the mid 2nd round. He's just not that good.
Heck, if you just watched him play, Clausen himself will tell you he doesn't have an NFL arm because he checks down so much. Or just look at the two numbers I think are telling. QBs with a low Y/C usually have a high completion percentage. QBs with a high Y/C sometimes have a low completion percentage (or are just that good). Clausen not only barely completed 50% of his throws but he had the worst Y/C in the league. His numbers were the worst the league has ever seen for a QB with enough starts (around 10-12) since Akili Smith. Clausen was trash in 2010. So lets end with the "he didn't get a fair shake," "we never saw him in a real offense," etc. stuff. Maybe that is true. But it still doesn't change the fact he sucked.
The best we could get for Clausen is a 7th round pick if we're lucky. Teams didn't even want him when he was in the draft, when he hadn't proven he sucked yet. Now that he has shown he does suck, I don't see how we could expect to get anything out of him barring him looking like Brady in garbage time.