Editor's note (02/16/2013): The combination of DC and Chicago keepers was artificially low because there is a gameweek where neither team plays. Avoid this combination, despite previous advice that it was the best combination to select.
Keeper selection is an interesting issue that has been explored dozens of times for other fantasy soccer games. The general consensus is to find two cheap keepers who rotate having good matchups. I'm a big proponent of this strategy as it allows us to upgrade our squads in other areas. The other strategy is to buy one premium keeper and one cheap keeper and play the premium keeper in the vast majority of gameweeks. In the official MLS game, my gut is telling me to choose the two-cheap-keeper rotation strategy because of the bonus points players receive for recoveries, CBI, etc.
I took the expected goals conceded each week by each team for the first 10 gameweeks and contrasted them with every other team. I then chose the lower value for each gameweek for each combination and used that as my choice keeper for the week. From there I simply added up the value for each of the 10 gameweeks for the following values. The values in red text indicate that there is at least one gameweek where neither team plays.
I also picked out the top 10 combinations for each price combination possible for starting keepers. There were a couple teams (Vancouver, New York, Dallas) where I wasn't sure who would be the starting keeper and would result in different pricing, so I used my best guess for each team. Combinations in yellow indicate at least one missing gameweek.
I should also make note that LA was a completely different team last year with Gonzalez in the lineup. However, even when I adjust the numbers based on their goals conceded with Gonzalez, they still do not have more than one combination in the top 10 overall.
The following keeper combinations have a week where neither play, so their numbers are too low:
Chicago/DC (missing 2 gameweeks in fact)