Great question. Here's what's gone into my opinion on Clausen:
1) First I want to put it out there that I'm an ND fan. I hope that doesn't automatically dismiss my evalution in people's minds. For the record, I wasn't a Powlus or Mirer fan and while I like Quinn, I can certainly understand him falling in the draft and he's a totally different QB from Clausen.
That being said, I watch a good deal of ND football. ND during Clausen's tenure certainly hasn't been a team that out-talents it's competition week in and week out. ND doesn't have many games where they simply "throw their jerseys on the field" and get a win, like OU, Texas, Florida, USC, etc. ND hasn't had much of a D and the OL has been average at best (very suspect at worst). Clausen carried ND offensively this year, he engineered 4th Qtr wins or put ND in position to win against Michigan, Mich St., Purdue, Washington, USC (would've gone to OT if WR hadn't fell), BC, UConn and Stanford. Did he crap the bed against Navy, absolutely. But that game was the exception, not the rule.
2) Statistically he had a junior season that was better than both Mannings, Rivers, and Stafford. There's a great breakdown done by one of the guys at Walter Football that I've posted before.
WalterFootball.com: The NFL Matt Draft - Matt McGuire's NFL Draft Blog
3) Clausen comes from a football family, he's had the experience of his brothers to draw on. He's also been the #1 QB in the country coming out of HS, now he's the #1 or #2 QB coming out of college. The guy understands expectations and pressure. Think being the Skins QB is pressure, ND QB has similar pressure
4) Clausen is a film rat and hard worker. Quinn was a gym rat, 25 reps in the bench isn't going to help you read a D, influence a safety and squeeze a throw into a tight window. Spending hours in the film room will. "Know your enemy and know yourself and you will never fear in 100 battles." Sun Tzu.
5) He's over 6' 2", height isn't a concern. He's over 220, size isn't a concern. Hand size....I've watched enough of him to see that he can throw the ball pretty damn good, "small" hands or not.
6) Clausen had great pro-style coaching, who's a better QB coach than Charlie Weis. Jaworski (whose opinion I respect) says both Bradford and Clausen have the skills to be NFL starters, so I don't see Clausen being a bust.
Clausen has above average NFL level physical tools (arm strength, accuracy), a high football IQ, and the attitude to be the guy in the spotlight, the guy that has to make the play. I think the "leadership" questions are a non-issue, there hasn't been anything concrete I've seen and Kiper (while not the all-knowing oracle) does have good connections within college football and he doesn't believe there's an issue.
Clausen is a franchise level QB. He's a guy that will be able to take an NFL team deep into the playoffs within 2-3 years. We have the #4 overall pick, a guy with a bunch of indicators that he will be a very good NFL QB is there, it's a no brainer he must be taken. Being in a high draft position doesn't happen often (hopefully) and to have a franchise QB there is an opportunity that can't be passed on.
If he busts, what have we lost...just a single 1st round pick. We won't have to trade up, or lose other players, or otherwise mortgage the future of the franchise. What if Okung turns out to be just a good LT, not Pro Bowl level? What good was the #4 pick then? We can get good LTs in a number of ways. A franchise QB is much harder to come by.