The Muslim Brotherhood is by far the most organized political force in the region. And even if they haven't been active in Syria itself for some time, I doubt the more secular-minded rebels can stand in their way.
I would say the most likely outcome, by far, is that (1) Syria will fall to the rebels, (2) the Muslim Brotherhood will call for democracy and elections, (3) they will brand Al Nusra and other AQ affiliates as anti-democratic and "extremists", which western observers will hail as evidence of the MB's moderation, (4) the MB will win said elections by a wide enough margin, (5) Turkey and Egypt will compete for influence over the Syrian MB, (6) Turkey will emerge as the winner of that competition, (7) under the influence of Turkish PM Erdogan, the Syrian MB will publicly announce its commitment to secular democracy, while quietly imposing sharia law and imposing dhimmi status upon the Alawites and non-Muslims, and (8) Turkey will use the Syrian MB to bolster Erdogan's anti-Israel credentials, much in the same way that Iran has used Assad up to now.
All of which is preparatory to an attempt, at some point in the next 20 years, to reconstitute the Caliphate under the aegis of the MB. If that is completed successfully, then the resources could, presumably, be brought together for the purpose of the final destruction of Israel.