Force commander, (With a name like that why are you not bringing up the Micronauts/Microman lines?) I am doing something sort of similar. Mine is a bit more comic book focused.
My guys are a copy of A.I.M. from Marvel comics and the Riflethings are being used as the muscle enforcer guys who have no scientific expertise. And I assume they are modified to be pain resistant, loyal, stronger, heal faster, to be completely fearless, and so they can be communicated with quickly or even shut down remotely, as the higher ranking scientists require.
For the scientists and their assistants I use Khurasan's Hazmat soldiers.
I am still experimenting with color schemes on one of them. He gets painted, I hem and haw, I add a little stripe, then he goes into the simple green for stripping.
I have several small robots that serve as support and observer/political officers for the scientists. I am using Triton Maco sub hunters from the Monsterpocalypse line.
I use a plastic UFO model for their mothership. When I get a good orange yellow metallic look that reminds me of 1960's four color on newsprint comics I will paint it.
I may also use triangular UFO models as stealthy escort craft that can shut down power in vehicles with a null-beam.
I expect that the fake A.I.M. will attack reactors and other facilities to grab tech, abduct large parts of a small town or mining camp's population for experimental subjects and recruiting, and just test their new weapons on small military bases.
I also have a few failed attempts at a Giant Brain leader one of whom looks like MODOK a little bit only he is seated on a little throne with treads. I am still working on these guys but one of them will probably be represented by the Ego-bot that comes with Mr. Brain. Why wouldn't a super scientist mutilate HIMSELF and call it evolutionary progress?
This is what the Ego-Bot looks like BTW, he's HUGE even in 28mm! the little Purple guy is Mr. Brain.
I am planning to have several divisions of the organization to have various focuses each lead by a giant brain guy. One will focus on giant intelligent and often cyborg gorillas. One will focus on turning humans into horrible bloated mutilated cyborgs (represented by the Mollock Subterrans from Monsterpocalypse and those things that I might kitbash) and one on advanced robots and pure exotic technology like grav-tanks and freeze rays.
Here are the mollocks. Don't they make great "wretched mutant cyber monsters"?
I am considering turning three Directorate Battleships into large grav-tanks/APCs and frigates into one man grav-chariots and a dreadnought into a command vehicle.
I am also working on some fake Hydra guys (who the fake A.I.M. guys sell arms too) who might eventually become the dominant terrorist bad guys. I am thinking about using some RAFM Traveller 15mm for them.
I think instead of a S.H.I.E.L.D. to face them I will have something more like G.I.Joe/Action-Man and there may be a Cobra-like Splinter force who went WAYY too far in fighting the fake Hydra guys and were decommissioned so they fled and became their own scary paramilitary menace.
Anyway I hope to have a decent force of fake A.I.M. guys online by October. I already have the Mollock faction worked out.