Here's the all time rankings:
http://cfbdatawarehouse.com/data/rankings/all_time_team_rankings.php
I consider them a matter of importance because they demonstrate the underlying level of support a program has. Things might vary over time, and some distant records skew things somewhat (such as Yale or Princeton's dominance in another era), but the tendency is for a football power to trend that way over a long period of time, such as Alabama returning to dominant form. I used these standings to argue that Texas A&M was a strong football program when some argued against their inclusion to the SEC (arguing, ironically enough they weren't good enough). Of course, Oregon is an exception, with their offense and Phil Knight fueling current success. It does, however, remain to be seen if that is sustainable over a long period of time.
What you are alluding to is nothing but PR problem, which of course other conferences have incentive to focus on. It is interesting, since the Pac 12 appears to play the second most difficult conference schedule. But, the sheer physicality of SEC play demands some sort of a breather. If you have an offense that's more spread out, that is more pass heavy as west coast offenses tend to be, you have a less physically grueling opponent. This is magnified as the season progresses. It might not even mean more serious injuries, but it means more bumps and bruises, more pain, more soreness, longer recovery times, etc...
Anyway, as a whole this notion is driven by a silly idea that a power 5 conference game is created equal. As the rankings I showed demonstrate, that's absurd. I won't take the time to do the ratings, but look up some ACC schools for example. Duke, Wake Forest, are they not (usually) weak teams? Simply being in the ACC doesn't change that.
This then gets into another flawed aspect of SoS. SoS is an average, however, for a truly elite team, it only really matters when you're around the top 50. So, an SoS calculation will insist it matters more to play #70 than it does to play #100, but does it really? Not when it comes to determining a champion. What does matter most however, is playing #10, #5, that sort of thing because those are the games that matter.