It is known that Brahimi finds the fragmentation of Syria's opposition the most difficult part of his job. One could add that the armed opposition is not independent but relies for its finances and arms on Qatar and Saudi Arabia. So if one group would decide to negotiate with Assad the likely consequence would be that the financiers will simply switch and support a different group.
All this financing is of course a violation of international law but I am afraid that complaints about that will achieve nothing.
So I think the most workable option is having the Muslim Brotherhood to negotiate with Assad. The Brotherhood doesn't represent all rebels but an important part of them does so. And as the present conflict is also partly a repeat of the conflict in the early 1980s a consent of the Brotherhood will give an important signal that a solution is possible. In addition, the Brotherhood is as a non-military organization less sensitive to foreign pressure.
It won't be easy to get the Brotherhood to compromise with Assad, but I think it is Syria's best chance. The Brotherhood is the only organization with enough authority not to see itself marginalized when it negotiates and compromises with the government. If it - with it grudges dating from 1982 and before - can reach a solution anyone can.