Do we still take him with the first pick if he has a good year at SDSU knowing that his mechanics aren't great?
This #1 pick really needs to pan out and be ready to be a full-time Major Leaguer by 2010.
I think you pretty much have to take him if he's the best player available, regardless of these concerns.
Comparing him to Prior, I think there are enough differences that it's not a terrible concern. I'm no expert on mechanics, but I can notice a few differences in their mechanics. Prior's arm angle at his delivery is much lower. It's close to parallel to his shoulder. Strasburg has a higher leg kick - the action in the legs is much different. His right leg lifts much more quickly. Prior's seems to lag behind his left leg for much longer.
Also, the comments there seem to challenge the general conclusion of that post.
I'm not entirely sold that Strasburg will be so injury prone, but it's interesting nevertheless. Just as you had, I once read that his mechanics were extremely refined/clean so I was surprised to find this.