Firstly, I expect that you're probably more likely, if anything, to get fed up with a NES whose proposed structure contains an extra 18 updates from the outset.
Secondly, I think that a lot of the problem stems from your overarching desire to - contrary to what you said at the outset of CIEN, that everything would be player-action driven - define the events of very different 19th and 20th centuries by the social and political norms of our own 19th and 20th centuries, which don't really fit in the world you are modding. I mean that, in order to mod a paranormal Brazil, you need to mod paranormally, as it were, rather than just trying to impose odd diktats that para-fascism and anti-war movements emerge necessarily in this period. As long as you keep on doing this, you will run up against the same problem: no world except the one we actually live in would have generated anything very closely resembling fascism, or anything very closely resembling 1920s anti-war sentiment (or, indeed, quite probably anything resembling very strongly the Great War). As long as you keep on trying to impose facets of our own world on a world that is not our own, you will find that it brings out the fact that the world doesn't really hold together on those terms.
Thirdly, I think, in continuation of this, that Brazil's inherent implausibility doesn't matter any more than it did in 1830. It only appears to matter now because our world has developed, and become complex, and had implausible features of our own world plastered onto it. If you weren't trying, in short, to make Brazil a real-life Brazil, then you wouldn't come up across such a particular problem.
In summary, I predict that, if you do what you propose by starting in 1000 AD and moving forward, you will generate an equally implausible world governed by logical inconsistencies between your own impositions of what ought to have happened in each century by the standards of our own world, and what the players actually made happen. The result will be nearly or quite as implausible, I think, as if you had just come up with the scenario yourself.
Fourthly, I'm not personally interested in joining any new NESes; equally, I don't mind much if this one dies, because I'd quite like to give up on NESing for the moment anyway, although I don't want to abandon the Confederation.
Anyway, that's my opinion, for what it's worth.