I got an idea that fits the Cult. Which is based on stolen technology units from Mental Omega.
The Smugglers Den contains powerful upgrades with eight technology branches. But they can only buy said upgrades once their Apothecary infiltrates their opponent's base. The reason behind it is that the Cult is stealing their opponent's technology and reverse-engineer it to use it against them. The branches representing the factions they infiltrated, including their own. It even fits with the name "Smuggler Den".
Due to this, each of the branches contains upgraded built to specifically counter the opponent their facing, meaning normally they would only go through one tree. Maybe even produce one or two specific units (like infiltrating the ARVN would give them a unit based on the Black Hand)
NOTE: These are meant to counter their opponent so they will be rather specific (and will likely be ineffective if they somehow face a different opponent) and overpowered (since they are meant to punish an opponent who is not vigilant)
ARVN: Not sure yet. But it involves napalm and maybe air superiority. If units are allowed then possible one based on the Black Hand (unit and/or faction in Tiberium Wars).
Reservist: Gives the Cult powerful AA weapons and/or aircraft. And maybe even gain access to Allied vehicles.
NRA: A lot of artillery and garrison-clearing weapons. And using both scrambler weapons and necroscience, possibly with units that are a nod (rimshot) to the Brotherhood cyborgs.
Vietcong: Stealth detection up the wazoo. And possibly Soviet vehicles.
PLA: Anti-horde weaponry and cloning. And possibly units that use nukes.
GLA: Similar to the Vietcong (here is where you put your suggestions). And GLA units not in Paradox such as the rocket buggy.
II: Anti-vehicle weaponry, similar to the Tank Destroyer Tactics in COH. Including a unit that could be based on the RA2 tank destroyer.
Cult: Tools built to counter themselves. And (I'll admit this may be out of line) a true mind control unit like the Mastermind.
So, @Metaltooth, @SlimTheSlick, @Daedalusfan300, @LtGenJackGranger, and @Weirdo4ever. Thoughts.