No, no, I get that it's a modernization of the old feudal structure based around divine right and allocation of power. What breaks my SoD is that the original Vers managed to accumulate a power-base quietly and quickly enough to avoid being nabbed by some group or other and used as a test subject and breeder to pursue understanding of how the tech works while also maintaining a population of Aldnoah-users that'll at least be stable in the short term, possibly longer if the genetic marker or whatever for activation doesn't "dilute" over generations without sufficient inbreeding.
Its heavily implied that the emperor being an Aldnoah user isn't natural, and was a result of some kind of experiment on himself (as he was one of the scientists who found it). But you are correct, if the emperor was kidnapped, it would probably be fairly easy to replicate his power (assuming of course that the power is genetic and not given by nanobots or anything else hard to find and replicate).
And more breaking of SoD: Apparently all Aldnoah tech activated by a given individual shuts down when that individual physically dies, even if they're revived later. Granted, it's an excellent insurance policy for a controlling dictator, but it's also a glaring weakpoint before the establishment of that dictatorship. What would've happened if someone had put a bullet through the first Vers' heart while he was walking around somewhere? Poisoned his meals? &c. Well, we wouldn't have a plot, obviously, because whatever support he'd gathered would be abruptly declawed.
Its important to understand that the empire didn't create any of the Vers tech, merely copied old alien tech. So yeah, if they could manage to kill all the royal family, it would do massive damage to the empire. Of course, its entirely possible that there is an artifact lying around somewhere that gives his power that would mean that killing him would be little more then a moral and political victory. Its also important to note that they didn't create or design the tech, so it coming inbuilt with a massive weakness for their uses isn't too odd.
My personal favorite theory is that the Aldonoh is like keys to your cars. The aliens used them to make sure that their vehicles would only turn on for them personally, and if a friend wanted to borrow one, you could give him permission to use it. And since once you use it you keep control of it until you go unconscious, no one could steal it from you even with the same ability without knocking you out (in which case they could probably kill you anyways).
Hell, why didn't the Terrans just load a slow-burn ship with nukes after the war and send it to Mars? If we can build things to crack Norad and the Aldnoah tech is apparently as weak as it looks to conventional arms in the absence of clarketech bullshit space magic, surely they could have just plastered the imperial palace or whatever until his royal blondness bit the dust?
After the war the martians had those orbital castles around the planet, anything military they tried to send would have been blown to dust. Not to mention that the martians would probably have used any attempt as an excuse to finish wiping out all the earth governments and cities ~20 years earlier.