The Muslim Brotherhood is the only organized political opposition in Egypt, because under Mubarak no other political parties were allowed to be formed. The only candidates allowed on the ballot other than those from his own party were all labeled "independents". Of course MB will be at the table, otherwise Mubarak's people will be sitting there alone.
If democratic reform is to take place, the first thing they have to do is allow the creation of opposing political parties. Once they've done that, there will be more than two people at the negotiating table, starting at each other with suspicious eyes. There will be a dozen people at the negotiating table staring at each other with suspicious eyes. You see? Progress!!