Kaos,
I think your theory of historical precedent has a very key divider to it. It matters 100% what you're replacing. There is no way to know to an exact degree, but you have a good idea when a player is "adequate" , a "liability", or is a "difference maker".
For example. When Texas replaced Chris Simms, everyone everywhere knew Texas wouldn't drop off, because Simms had been merely "adequate" at best. It was very reasonable to assume Texas could be at least "adequate" again the next season, even before seeing what the Chance Mock/Vince Young combo was capable of.
To me, Alabama 2009 actually goes with the "rule", and is not an exception to the rule. The fact is, John Parker Wilson wasn't a special talent. He was more "adequate" than a "difference maker", so replacing him with "adequate" was not going to create a huge drop off at the position.
2008 Wilson - 121 passer rating, 57.9 completion %, 2243 yds.
2009 McElroy - 140 passer rating, 60.9 completeion %, 2508 yds.
The truth is, if you go back through history, when top programs are dealing with an "adequate" QB (often), replacing him with another "adequate" QB is pretty common. It's actually more of an exception to the rule when they go from "adequate" to "liability".
To me, Todd was adequate, and for someone (me) to expect that Malzahn can come up with at least "adequate" from what we have on the roster seems to me to fall directly under "reasonable", as far as expectations go. Look at what he just did at Tulsa.
In 2007 Paul Smith had a rating of 159 and threw for 5,000 yds. In 2008, Smith is gone and a new guy steps in....David Johnson. In his first year, Johnson has a 178 passer rating and throws over 4,000 yds (they ran the ball 1500 more yards, so the 4000 was still very impressive).
Your "historical" reference applies to situations when a team goes from a David Greene to a DJ Shockley.
Or from an Andre Woodson to a Mike Hartline.
Or from a Sam Bradford to a Landry Jones.
Or from a Vince Young to a Colt McCoy (there's your exception).
Or from a Matt Stafford to a Joe Cox.
Or from an Eli Manning to an Ethan Flatt.
Or from Troy Smith to a Todd Boeckman.
What's more normal is going from a Matt Mauk to a Marcus Randall.
Or from a Joe Ganz to a Zac Lee.
Or an Erik Ainge to a Rick Clausen (and back to an Erik Ainge).
Or from Sean Glennon to a Tyrod Taylor.
Or a Will Proctor to a Cullen Harper.
Or an Andrew Hatch to a Jarrett Lee to a Jordan Jefferson, mixed with some more Jarrett Lee.
We just had Joe Ganz/Will Proctor/Sean Glennon, not Eli Manning/Sam Bradford/Vince Young.
Todd was "fine". To expect to replace him with "fine" seems very reasonable to me.