Here are the issues I have with Clausen:
When he throws off his back foot, which is quite often, he loses all velocity in his passes. Let's look at two examples from the Pittsburgh game. Firstly, Clausen takes a snap under center on his own 23-yard line. He drops back, eyes up his best receiver Michael Floyd and without making any other read floats a deep pass down field. It's under-thrown off his back foot and simply hangs in the air. Floyd is double covered, so it's not a great read anyway - but the fact it's thrown so gently makes it a jump ball up for grabs. The defensive back catches the ball and it's a turn over.
On the second example, Notre Dame are 4th and 1 in the third quarter. Clausen uses play action before dropping back. The Pittsburgh defense completely bites on the PA, allowing Floyd to run a deep route straight down the middle of the field. He's completely open and a well thrown pass leads to an easy touchdown. Instead, Clausen under-throws off his back foot, again floating the ball high into the air. The air time on the pass is excruciating, forcing Floyd to physically stand still and wait for the ball to drop. Of course, by the time it lands three defensive backs have reacted and instead of a touchdown it's merely a completion. However, that was such an easy throw to make and it simply must be a touchdown.
It should bring his arm strength into question. However, when I watch Clausen drive the ball off his front foot there is some velocity. But this only happens on short slants (Clausen throws an outside slant more than any other pass). I'm not sure he can make big throws down field with the same kind of drive. This is a big concern because whenever he throws deep, it tends to be under thrown or too floated with little or no velocity.
My next complaint is about his mechanics and most of all, his side-arm throwing motion. In all honesty he gets the ball out nice and quickly. However, the fact the ball is coming out at shoulder height (and he isn't a huge guy - 6'2" at best) leads to all kinds of problems. In this game alone I saw two tipped passes and a throw that hit one of his offensive lineman smack on the back of the helmet. There were also four occasions where Clausen just simply threw the ball too low. His action is such that the ball generally projects downwards and this led to some drops because the receiver is having to dive to the ground to get the ball. NFL scouts and GM's want to see guys throwing the ball as high as possible - that's why Mark Sanchez made a concerted effort to correct his mechanics before the USC pro-day.
I also didn't like the way he dealt with the screen pass. On one occasion, he completely misjudged the throw and made an ugly short pass to a receiver who was only a matter of yards away. The ball fell short by a good couple of yards. On another attempted screen, he made an exaggerated pump fake to the left before running back 15 yards behind the line of scrimmage. By the time he'd finally got round to passing the ball, the Pittsburgh defense had been given an age to react and had pushed forward into the backfield. The pass receiver was snuffed out quickly for a nine yard loss.
Now, it's easy to see why Clausen has put up nice numbers this year (21/4 TD/INT ratio). He doesn't make a lot of bad decisions in the short game that lead to interceptions. A lot of his passes are high percentage outside slants and we have to remember that he's throwing to two of the better receivers in college football - Michael Floyd and Golden Tate (although admittedly Floyd has missed time this year). But I saw no evidence of a guy who can come into the NFL and put up big numbers quickly. He can't keep throwing the same outside slant every week to the same guys, occasionally floating passes downfield hoping something comes off. He'll be an interception machine throwing downfield like that.
He needs to work out the kinks in his mechanics - try to release the ball a bit higher and throw off the front foot more. Simply coming from a 'pro-style offense' and having nice stats isn't going to mean anything at the next level until he does. Personally, I wouldn't touch Clausen early and even with Seattle's second pick in the first round he'd have to be viewed as a substantial project.