If there was no campaign (and we didn't know that it is based on a faction in Yuri's Revenge), the Epsilon would be mary sue as well, because they do seem to have hi-tech units with ufos and airplanes that look like spaceships. One would think that the Epsilon are aliens if not known ontherwise. :V
The Epsilon is unique. They combine very outdated and outright primitive stuff, like the obsolete Lasher tank, the Gatling Tank that looks like it's cobbled together from scrap metal, a friggin catapult that throw bombs of toxic stuff with rather advanced stuff like those that you mentioned. Then there are the Initiates, who don't even have a weapon to begin with, and have to resort to using pyrokinesis. Besides being the first part of their training as psychics, I wouldn't be surprised if it was the result of the Epsilon being short even on small arms and ammo supply (this would also explain why they have archers), then these things remained in their arsenal even later, because they proved to be quite effective. Or the Bio reactors, those things too are born out of necessity, I believe, being fed up with the inefficency of coal, and being cut off from more advanced techologies such as Tesla and Nuclear power, the Epsilon started using organic stuff as fuel, Matrix style. It's just pure genius, evil genius, but still genius. Epsilon shows a clear technological improvement as they progress, both in the storyline, and in individual games as well, and so do the Allies and Soviets, while all of Foehn's stuff is very advanced to begin with.
While the Soviets put a trench coat on a man and give him a PPSh, and call it a soldier, the Allies give a man some flak armor, an SMG and a LMG, basic training and call it a soldier, the Epsilon teaches their followers how to set things on fire with their minds and gives them fireproof suits so they don't burn themselves accidentaly (there's also some sort of device on the concept arts, but it might be something as simple as a stimulant dispenser).... the Foehn, they give their basic infantry friggin exo suits, that would be tier 2 or 3 for anyone else.