Agreed, but for now, there really isn't a better way to get a quick evaluation of a how a qb played without actually watching the game. Aikman (I think it was him - it may have been another former qb/commentator) has a qb rating that seems more fair, but I forget how he comes to his number.
You have to look at the stats to a certain extent tho - if someone only throws for 2000 yards and 12 tds a season, they don't deserve too much praise, and you can't justify it by saying "he's just got too good of a running game to put up numbers." If his running game is that good, to a certain extent it should open up the passing game some, which would result in a higher qb rating.
Finally, it is impossible to compare stats of qb's from different eras - the league has changed way too much to compare Peyton to Staubach or any other of the old timers. Even the recent ones don't always have good numbers - is Drew Bledsoe better than Dan Fouts and Joe Montana? He has more passing yards! Is Phil Simms better than Steve Young? You see, statistics can be misleading, especially when you consider the length of a player's career. Would John Elway have played so long if he already had 2 rings?.... ehhh, that's debatable, but I would guess he would have retired a couple years earlier because he would have accomplished all he wanted.
Just remember - Statistics don't lie, but liars use statistics.