The simplest answer to this question is that I believe Auburn and Missouri switching places would unquestionably be better for the conference overall. I also think it would be better for Alabama if they dropped the annual game, and it could be better for Auburn as well.
The reason this won't happen is also part of why it might not be a good idea for the two teams to play every year, there's too much emotion wrapped up in the game. It's become spiteful, and the lengths people to go have become unhealthy. A good rivalry is one of mutual respect, not hatred. The sad part is it could get worse, but in either case people have an emotional attachment to the rivalry that defies logic. They want that game, no matter what. They want to cheer against Auburn no matter what. I once denounced a lot of Auburn fans for cheering against Alabama rather than for Auburn, but I've seen the same behavior from a lot of Alabama fans. They cheer against Auburn even if it's in Alabama's best interests for them to win. They want the Iron Bowl to be played, even if it's not good for Alabama. They're so caught up in the spectacle that they can't seem to see beyond it. But, when we have fans making death threats after this game? It's just not good...
In terms of the conference, the East and West became unbalanced prior to the addition of Texas A&M. The problem was it was set up for the East to be top heavy, but if the teams at the top are not elite (Florida, Georgia and Tennessee), the teams at the bottom (Vanderbilt and Kentucky) are incapable of picking up the slack. This became magnified when Missouri and Texas A&M joined. Missouri has in some ways become the symbol of the East's mediocrity, while the fact that the bottom team in the West nearly knocked off the top team in the East really says something. Does anyone here really think Alabama vs. Vanderbilt would look anything at all like the Arkansas vs. Missouri game? It would have been a bloodbath. This imbalance is unlikely to change anytime soon, as Texas A&M opens up a lot of recruiting territory to teams in the West. If this issue isn't addressed, the danger is the SEC West continually beats themselves up while the East produces poor representatives for the conference (Missouri after all did lose to Indiana). I don't see any other ways to fix this problem and make any sort of sense geographically. Otherwise what do you do, swap Vanderbilt for Arkansas? In either case, the SEC simply doesn't need this game, as the fact that it's been played on ESPN a lot lately attests to.
Alabama stands to gain from freeing themselves of the Auburn game, in part because it's generally a bad situation for Alabama. Someone pointed out that Alabama hasn't beaten a ranked Auburn team in a long time. There's a good reason for this though, this is the last game of the regular season. This is a game that's hyped up a fair bit, it's never the type of game a team overlooks. Unfortunately though, since it is the last game of the regular season, the loss also really, really hurts. The teams have been fortunate that it hasn't caused more chaos, but for instance this year we're faced with a scenario in which this game can do no good at all. All it can do is knock Alabama out of the playoff and the SECCG. Alabama stands to gain nothing from this game, much in the same way they stand to gain nothing from this rivalry. They don't need Auburn for anything.
Auburn on the other hand has become married to this game. They need it to make them relevant. Their recruiting often benefits from getting players Alabama can't offer scholarships to, they provide an alternative in-state to people that are tired of all the Alabama hype. They do well as an alternative. However, the other side of that equation is they have perpetually doomed themselves to being the lesser program. By actively participating in this sort of relationship, they are accepting their status as a lesser program. So, if they ever really did want to see if they can really establish something on their own, going to the East and leaving behind the rivalry game is the best way for them to do that. Their schedule would become easier, geographically it would make more sense, but I think Alabama means way too much to them.
