I’ve seen a fair bit of comparisons between the two orders in question and the Nazi party. Let’s get some of the intricacies straight, because the story itself is pretty heavy-handed in explaining some of them to us. Actually, the story is heavy handed enough that the blunt answer to the topic’s question is “No, definitely not, end of discussion.” But we’ll go for the appropriate debate approach instead:
The Meek could be easily compared to the Nazi party. They spotlight themselves as the unfortunate, the unpowered, the hopeless, the underdog against a major threat. At the same time, they have extremely wealthy members and powerful patrons. They manipulate the political systems and national moods in order to place key people in positions of power, and they use the same systems to place key people in positions of power in the industrial sector. They end up rich enough to finance and operate a floating city-state and construct legions of highly enhanced battlesuits, as well as equip unpowered people with the technology to imitate powers.
The Meek are not the underdog in a fight against the powered any more than the Nazis were the underdog in a fight against some imagined Jewish conspiracy of global domination. They both just paint themselves in a shroud of propaganda in order to gain followers from the disenfranchised, who can be in turn manipulated and brainwashed.
The InfraOrder is actually much closer to some kind of radical Bolshevik/Anarchist movement. They are the poor, the desolate, the working class. Despite their powers, they are the disenfranchised and the downtrodden. The question whether or not they are worse off than unpowered poor people is left in the air in the story, but one would assume that they would be around the same level. InfraOrder conducts terrorist and insurgent missions in populated areas, their ultimate goal to turn everyone into an image of themselves in a desperate attempt at creating solidarity.
The InfraOrder is in turn manipulated by the Meek (in the Hero Project) to become another highly prominent scapegoat and target of hatred. Much like the communist parties of 1930s Germany, in fact.
Now to other points:
The way you tend to refer to the powered heroes and villains in this equation seems to me like you’re placing them in the place of the bad guys. Alright, I’ll concede that luxurious apartments in the richest part of the city is a bit much, as are the paychecks involved, but that necessitates a cultural and political change, not a full-blown genocide.
They did not take the fame and wealth from anyone, although it could be argued that at some point they should have paused to consider the ramification in a bigger scale. Powered people were slung into fame and fortune because of heroics, which is not at all uncommon in our day either. Hero worship and social media praise/condemnation waves are commonplace (look at Ronda Rousey for example) and it is ultimately the public who put these figures onto a pedestal. Yes, there’s competition as to who gets the most of that pie, but that would take place no matter what the level of wealth and fame would be. There are always people who would do it for wealth and fame instead of ideals, and that is an actual gameplay mechanic in the whole trilogy.
Just like in all hate groups and populist movements, there are people within the ranks with moderate views, and who genuinely believe they are doing the right thing. Most of the movement may be completely oblivious to the fact that their movement is actually advocating extermination, because they are blinded by their selfish interests. Hell, the leadership of the movement might hold some great ideas that would help disenfranchised and poor citizens across the nation. That still does not make it right to advocate for genocide, or forced mutation. The end does not justify the means, especially when there are much more moderate and rational options to be taken.
Your point about government corruption is moot. We know the story takes place in the United States of America (albeit many many years in the future) and we all know the government there is corrupt, or at least incapable and gridlocked. That requires political action from the masses, whether that take form in a revolution or simply voting out the bad apples. That does not necessitate or condone genocide or mass mutation of the general public.
There is also a gap in government involvement in the United States to what you’re advocating. The government does jack all about investing into poverty-stricken areas. That is very much a state issue, at least as far as I have understood how the US system works. Victon very much skipped the most important role in that way: he was never in state-wide politics, just Millenial City affairs and eventually federal-level.