I really like the idea of haveing a nemesis for the SG but I think that this should be a series of missions... perhaps 20-30 long... that has everything con purple. This would mean that everyone in the SG can contribute.
The other thing is that I think having the founder as a seperate rank is a good idea but do it by account so that their other toons are affected too.
My other thought is to have missions customisable by leaders. I think this would work best with a window that has certain set options to choose from. ie, choose map (ware house, caves, Orenbaga or lab), chose level (1-5, 5-10... etc) choose enemy dependant on level (1-20 gives you hellions/clocks/skulls/council/vahz, 20-30 is Tsoo/council/freaks... etc) Then a space to write the story and add a boss name and voila.