Quoting PossiblyImpossible,
Like it or not, WCG is one of the highest level venues for RTS there is. Which games end up on the line-up is not determined just by money. If CnC3 was placed on the lineup before it was released, then it was placed there by virtue of its Beta Gameplay. Games are played at WCG if they are deemed to be competitive and entertaining enough to be placed there. Similar selection processes are used for other venues like CAL.
No. What ends up in WCG is determined by player base. Guess which RTS have the largest online player bases?
Starcraft, AOE3, CnC, Warcraft 3.
Why aren't CoH, DoW, Rise of Legends, or heck, AOE2 in WCG? Not because they aren't competitive or capable of being so...but because they don't have a large enough player base or community to warrent them being there. SupCom: FA falls into the same category as these games - they simply don't have the community size for WCG to consider them.
However, I'm not saying there aren't other considerations for inclusion, though (seriously, what are Asphalt 4 (Mobile) or Red Stone (PC)?), but popularity is of the foremost importance.
(btw...fyi, apparently CnC was completely fubared balance-wise on release (not that SupCom was either) - its presence in that years WCG certainly was not because it was deemed a well-balanced game at the time)