The SAGE engine is a marvelous thing, of course it does have its fair share of flaws.
The premise is simple, if we were to create our own version of SAGE, what sort of features and adjustments would you make? Obviously, first thing is the removal of the arbitrary 128 upgrade and 15 AI limits.
Personally, I'd have factions be contained in their own modules much like MUGEN characters where all their assets are contained for easy additions.