Who commands the Radam anyway? Clearly, it's not the Tekkamen, since they're only created right before an invasion and only serve as temporary officers. And the bugs are too mindless to create and employ such advanced technology as the one used in Tekkaman armor.
Presumably, the Radam Brainslug that was in Kengo/Omega.
There was probably at least one Radam parasite wired into the ship the way Omega was wired into the Argos, which was handling the trees and Radam-juu that ate the Aibas. The mother ship had a small token contingent of Radam-juu to capture some Tek-capable beings, after which the Tekkamen would oversee the spawning of the invasion force proper, including parasites, trees, and Radam-juu.
Here's a big one. How did D-boy get his crystal back between Tekkaman Blade and the sequel? I believe it was supposed to be touched upon with Missing Link, but it would have been nice if the actual series explained this better.
Well, humanity have clearly got quite solid understanding of Tekkaman tech during Time Skip, as evident by creation of Earthen Tekkamen and even a serious modifications to primary weapon system - namely Reactor Voltekka. It's not too far-fetched assumption at this point that they discovered the trick to fix D-Boy's crystal.
The thing is, the second season was not supposed to be there - The Missing Link OVA was supposed to be the end of the whole thing, and there changing humans into Tekkamen was supposed to be dangerous as all heck, with nobody being reckless enough to try mass-producing them. And as for the crystal, the thing is - we don't know anything about those. We only know that they need to use a crystal that is "complete" even though just putting all the shards into Pegas was enough to emulate that, and that having a fragment of another crystal strengthened a Tekkaman's power temporarily in exchange for gradually destroying the fragment, and that the plants interact rather weirdly with Tekkamen who have their own crystals. Thus, it's possible that either the crystals can regenerate given time, or that D-Boy decided to use one of the flowers to regain his power when it was necessary (though getting an artificially created crystal is not out of the question, just unlikely).
It needs to be pointed out however, that despite humanity's advancement in the use of the Tekkaman technology, the Radam versions are clearly superior, as demonstrated by Tekkaman Dead and Blade. And as inferred about Blade during the clips shown during Missing Link.
This troper still wonders to this day whether Toshiyuki Morikawa really did break those two poor microphones or not.