Lets take this back to basics. What are your design goals for
a) How teaming should work
You mentioned mutants earlier, do you intend to have all player play at the mutant faction (FYI, we don't have "mutant GDI" and "mutant Nod", only "mutants" in general, who are called the "forgotten"). Give us a better idea of what you want to do and we can suggest ways to make it happen.
b) The Obelisk
Is it intended to be neutral, and thus hostile to both teams? Or is it owned by one team at a time? What should a team do to make it friendly / neutral towards them? Should it remain friendly / neutral forever? Until the enemy do something? For a limited amount of time?
c) Any other special features you want to implement.
I think some of the dicussions in here thus far are missing the context required to give the right answers