Since I got the history lesson here, allow me to make a call on this: The Prophecy add-on has the most powerful fleet for a few key reasons:
(Comparisons are Ops and Pre-Battle of Earth)
1) Ships:
The warships are far more powerful, consisting of the full Prophecy era as well as refitted wartime ships (if I am incorrect in that assumption, then Confed is inherently foolish and should be beaten senseless)
Huge advantage: SO Fleet
2) Preparation:
Since Prophecy has already played out, Confed has the info on the Nephilim and have now prepared in some form for this new assault. However, the old Confed was already in a state of war, plus we knew almost all there was to know about the Kilrathi
Edge: Battle of Earth era
3) Leadership:
Almost everyone in a command position is a veteran of the Kilrathi war, and with the exceptions of Admiral Tolwyn and Christopher Blair (please correct me if I'm wrong), the leadership still has a good idea of how to fight a war. In addition, the younger commanders (i.e. Stiletto, Frosty (I like Dallas' handle for Casey)) have cut their teeth, and though still just a bit green, will never pass CAG inspection again (remember: a combat ready unit has never passed inspection; an inspection ready until has never passed combat)
edge (though very small): SO Fleet
Overall: If both fleets were to engage each other, the wartime fleet would be wiped out, but the SO fleet would be severely damaged. I'll call for the SO fleet to have 6 surviving warships, all with heavy casualties.