Okay...
*sigh*
I'll start with a disclaimer: I'm not 100% sure that I'm really crabby about what I'm about to say, or if I'm just P.O.ed that you're starting over and that therefore getting to the next update off the end of the story will take all that much longer. So, y'know, get the salt shaker out and take this with a few grains.
But.
The prologue stinks, from a plot perspective.
I know, you're trying to set forth a shift of the TSAB governing body into Darker and Edger territory, and I love a good political conspiracy as much as the next guy, but the bottom line is, this could not have happened this way. Not with the way you've proceeded to start the story itself.
That is, the TSAB launched a brutal, bloodthirsty war of conquest on Earth (well, and everywhere else as well, but that's not really relevant to my complaints) which resulted in heavy violence on both sides, and apparently Nanoha and Hayate...didn't give a damn? 'Cause there they are, still embedded freely in the TSAB's military structure, pursuing their careers, happily raising their families (well, if you count the Wolkenritter as a family...). Not only didn't they rise up in epic revolt, but they also didn't even object loudly enough to hurt their career plans or create lasting psychological scars to bug Vivio? Honestly, I can see how someone might not be willing to join The Rebellion in a likely-to-be-ultimately-futile conquest, but Hayate is still on the Now-Suddenly-An-Evil-Empire's payroll in an administrative position? The violent takeover of her home world out of sheer greed for power, the wanton slaughter of assorted countryfolk and possibly friends and family, and the accompanying firm establishment of the fact that the TSAB is now a Genuine Force of Evil wasn't even enough to motivate her to quit her freaking job?
Incidentally, the way you've set up the government doesn't work either. Veto power (particularly if a society is stupid enough to allow it to exist without the ability to override it in some way) is a potent way to castrate a legislative body, but conversely the Adminstration Act, as you explain it, would have to be passed by that legislative body. If Hunter was given the ability to both veto legislation and create it by edict, that makes him a dictator, and while it's certainly reasonable to believe that a dictatorship could rise out of a chaotic situation, it's not reasonable to believe that somehow a constitution which openly provides for dictatorial powers could be snuck under the noses of a party which exists for the sole purpose of supporting rule by a non-dictatorship.
So...um...I hate to say this, but my advice is to take a red pen, draw a big X through the first six paragraphs, and start over. Honestly, the actual chapters don't present anything resembling the kind of major societal upheaval that the prologue represents, so I'd strongly suggest stepping back, ramping it down, and starting that backstory part over. Remember, too, that if you turn the TSAB into a heavy-handed totalitarian, warmongering state that there will be an inevitable impact on its citizens in daily life (the kind of state that imposes its will by violence on all foreign nations it encounters simply cannot run its internal society on the peaceful, basically "good" basis that you present), and through the many chapters of your original version as well as the revised chapter here, you--rightly, in my opinion--do not present that.
Actually, I'll boil it down into one sentence:
Vivio is too much of an innocent naif to have grown up in Stalinist Russia.
(I was going to say "Nazi Germany" but not only didn't I want to Godwin's Law my own review but it isn't accurate; you didn't present the TSAB as having an ethnic or cultural bias anyway but just as power-hungry imperialists. You could almost get away with a parallel to the European powers as they expanded their global empires from the 15th-mid-20th centuries, but the sociocultural biases don't exist within the TSAB since it's already a multicultural federation of a wide variety of cultures and groups...which, incidentally, is the major objection to a "we've turned into imperialist nutbars" agenda anyway).
And remember, you can do a story where the heroes rebel against sociopolitical authority without having to make that authority an over-the-top, cartoonish evil. If you're American, I'd suggest looking at, for example, McCarthyism in the 1950s (or, as some cynics would say, the George W. Bush years), or the pre-Civil War tensions over slavery and states' rights in the 1840s-1850s, or the tensions during the Vietnam War for examples of how a society rooted in basically good intentions can nonetheless have elements of it take a sharp wrong turn in practice in such a way as to affect, harshly and dramatically, many lives--perhaps even demanding the action of heroes to correct. Other nations have had their own moments, of course, but that's just a smattering from a U.S. point of view; I don't want to turn this into a political discussion over what constitutes justified versus unjustified actions by different nations and cultures!
*sigh*
Okay, that takes us up to paragraph seven. And the good news is, once the story itself starts, you're doing fine. I like Vivio, Falling Soul, and their interactions with Zaffy. The opposition is better fleshed-out and presented than in your original version. I like that you're introducing the OCs earlier (though the physical description of Kaon Jin seems a little forced, given that the scene is a one-person one from her POV--I have a suggestion for that, btw; PM me if you want my advice...on the other hand, you may prefer that after my rant on your prologue to delete me from your "friends" list and toss any printouts of my work into the nearest wood stove...) and making Zen...well, less Zen-like.
So...yeah, I'll keep right on reading more, but I'd really advise tightening up that historical backstory into something that works better with the way you've expressed the fic itself, because the fic is quite good reading and doesn't deserve to get bogged down by the weight of its own background.