That's a whole lot of questions and I'm sure they are loaded questions too but I'll take a crack anyway.
Drew Brees HAD a subpar arm. Then he showed up to camp in 2004 having improved his ball velocity by 20%, consistently. He improved his distance throws and his velocity. How? He simply got in better shape, and broke down his throwing motion. Now I will sit here right now and swear to you he has an arm that is comparable to those of Trent Green, Rex Grossman, and Tom Brady. That probably ranks his arm somewhere between 25 and 30 among the 35 or 36 starters/pseudo-starters in the league. That isn't bad. It's definitely workable. Would an armstrength whore like Scott Linehan accept that? No, but Mike Mularkey and Nick Saban would.
The shoulder injury is concerning, but it is good to note that it is NOT the torn rotator cuff that has severely affected guys like Pennington and Griese over the years. It was a torn labrum. Those happen, and the prognosis is generally much better for torn labrums than torn rotator cuffs. For one thing, to my knowledge you aren't as likely to suffer another torn labrum as you are to have further rotator cuff problems. Is it concerning? Absolutely. But it isn't a dealbreaker in any way.
As for Denny Green, he runs an offense that simply is not compatible with Vince Young's talents. They've spent a lot of resources upgrading that WR unit (1st rounders on Larry Fitz and Bryant Johnson, 2nd rounder on Boldin). Put simply, Vince Young doesn't fit as Denny's kind of QB. He's cool with a guy who can run, but he wants guys who have stellar passing ability and can maximize on his ultra talented receivers. Vince Young, not unlike Mike Vick, is a WR minimizer. First off he's not a good vertical passer and Green likes to have a QB with a gun and nice touch that can hit receivers vertically. Also, Vince's runs take away from his passes, which for Arizona would be kind of like trying to feed the entire Brady Bunch out of one bowl of cereal. Denny recently said he won't spend big money on a FA runner. What does that mean to you? To me it means he's staring at LenDale White and saying he's as good as ours...and if the Packers take him first? Then DeAngelo Williams is theirs. And if not, he desperately needs line help and well I'll be there's Winston Justice sitting right there, troubled black youth with all the potential in the world that he is, perfect for Denny Green. Green won't pick Young. I'd stake a lot of money on it. I bet he would take Brodie Croyle though...or Reggie McNeal...even Omar Jacobs. I'd be willing to bet a lot that Omar Jacobs is Denny Green's guy, actually.
The Dolphins wouldn't take Young because Nick won't take on an idiot at QB, plain and simple. You have to be smart enough to understand the scheme. If Scott Linehan were here things would be different, but when Scott left the emphasis got placed on the Tom Bradys of the NFL, not the Daunte Culpeppers.
Danny had a low wonderlic, but not as low as the 6 that I am quite positive Vince scored on his first test. Also, Danny NEVER had to have an offense dumbed down to him. Is the wonderlic an absolute determinant of intelligence? No. Frank Gore scored a 6 but he actually has a documented learning disability and he's far smarter than his testing indicates. Danny Marino, for whatever reason, scored low but came across high in intelligence in interviews and certainly in his understanding of the offense and the things going on with the football field. Vince Young's score is low, so that means you search for OTHER cues to give that score legitimacy, or illegitimacy. What are the other cues, though? Poor decision after poor decision since the Rose Bowl? Deciding not to show at a scheduled meeting with endorsement companies? Deciding not to show at a hodge podge owners party where he would have had the opportunity to put on his sunday best and schmooze with potential employers? Hiring a backwater agent with no experience preparing players for the draft? Spouting off at the mouth about how scouts don't need to see him run because they know what he can do running, but saying he'll throw at the combine only to later reneg on that statement? Or how about not even bothering to hire a position specialist to coach him up until a week before the Combine, when it was too late already?
So basically, you're staring at a poor wonderlic showing and saying ok, we need to take OTHER cues from this guy's life to see if we think he has the intelligence to run a complex NFL offense, to break down complex NFL defenses, handle himself as a professional, lead men, etc. I'm afraid the other cues have just not spoken highly of him at all...and the worst cue of all is the fact that Mack Brown had to dumb down the offense and simplify it to maximize Vince Young's talents. I love when he tried to say in interview that the Longhorns ran a pro style offense. A shotgun offense that revolves around the zone-read? I can't think of a more non-pro offense.
There are things that separate Vince from previous examples of a guy showing poorly on the wonderlic, especially Dan Marino.