Compared to the normal Thor, the Super Thor is much more durable thanks to its energy shielding. In terms of weapons, in addition to the 'Mjölnir' lightning beacon, the Super Thor is armed with five missile launchers, five prism refractors, a pair of 360mm cannons and four anti-air laser cannons that make it much more of a threat.
When the Russians attack the facility where the Super Thors are manufactured, all of them are destroyed alongside all related data, preventing the Allies from mass producing them.
The Super Thor is programmed in a rather simple way. By 'loading' five Guardian GIs, five Siege Cadres, two Aeroblazes and a Battleship into an open-topped Thor Gunship, allowing all these units to fire from inside.