There's a reason that Flynn was taken so late -- the sixth or seventh round -- and Griffin is projected to go in the very top of the first round. Griffin is the much better pro prospect.
That said, I think the way to evaluate the two is based on risk. Flynn would only cost Miami $$$ if he's a bust. That's hardly any risk. Trading up for Griffin and having him bust would probably cost Miami big time for 5-10 years. That's a big risk.
When the Bills traded up for Losman in 2004, he cost them a 2005 first, a 2004 second, and a 2004 fifth in outright draft picks. Those were players they never had a crack at, including Matt Schaub who went in the 3rd round of the same draft. Moreover, having Losman and attempting to develop him meant that the Bills didn't even look at better QBs who came along in later drafts: Aaron Rodgers in 2005 and Jay Cutler in 2006. They also weren't interested in the best FA QB ever: Drew Brees. Finally, in order to give Losman every opportunity to develop, they released Drew Bledsoe whom they gave up a #1 for in 2002 and who went on to have a couple of good seasons with Dallas before he retired. The Bills are still paying for the Losman pick.
The happy thought is that the Jests are probably going to find out the high cost of trading up to take a first round QB bust, too. Sanchez has "bust" written all over him since virtually all his problems stem from the fact that he can't read defenses because he doesn't process what he's seeing on the field very well despite having more than 50 starts.
