An obvious observation:
The more players of the same faction at a table, the easier it is to complete this faction secret(s) mission(s).
Thus, for convention play, we should limit the number of characters of the same faction at two per table. If you have 3 or more of the same faction the table, these guys controls the party agenda...
(In the event were this situation is unavoidable cause we do not have all the time we want for marshalling tables, then we should instruct the GM to be 'thougher' on secret mission objectives).
Something else:
It could be interesting, however, for only one slot of a 'big convention next summer' , to marshall tables with every character belonging to the same faction! Think it would be quite fun to meet some of our 'faction brothers' in a special scenario. Of course, faction objectives would be quite hard to meet in such scenario...
For the Glory of PFS.....!!!