There's so much in your post I like here that its hard to know where to start.
Also I think they should set their number higher. Looks like their criteria is 80...but who is to say nations now at 80 or 120 etc. wont drop to 60 or so in the future? I think they should set the bar higher, around 200 or so, and really have few 'macro' nations.
For the merged nations they are talking of numbers around 80-200 I think. I think they should make larger groupings and pull in more nations, setting up to around 1000 per merged nation, about Utopia size. IF the game expands that shoudl go up, but even if it shrinks it should stay several hundred.
I'd possibly go even further and say that any nation with less than 500 nations should be looked at. The top 6 or so nations in terms of numbers have 1000-1800 people in them. Ideally whatever new "groups of nations" they come up with should be looking to be 500-1000 in numbers at least. The game would simply function better in so many ways if the leagues were similar sizes. If this means removing nations' leagues, then frankly, so be it.
For the macros, maybe around 40 teams now, and not balanced in the regions. Draw them into group stage like world cup of basketball or soccer. Maybe 8 groups of 5, or 5 groups of 8, something like that. do a round stage, send up the best X number of teams from each group to make a 32 team knock-out like a real world-cup of soccer etc. Do it every season.
Perhaps two classes of NT, as you describe it, Macro and Micro. If I understand you correctly you'd have two similar competitions. How about if the bottom team in each of your Macro groups relegates to the lower level the next season, to be replaced by the top teams from the so called Micro groups. If seedings initially done by WR, then I see this as being a way to have real competition for both groups.
Think like cricket or rugby world cup where they just use the nations that those sports are popular, not balanced regionally at all, doesn't need to be.
In reality competitions are regional for a couple of main reasons. Travel costs and of course the enjoyment of beating your neighbour at sport instead of going to war with him. Though there was the football game that started a war but that shouldn't happen here. Anyway my point is, here there are no travel costs so it seems almost stating the obvious that you're absolutely on the ball here.
Even speaking as a former NT coach, I see the NT as being less important than club level. Its a pleasant addition but what is best for the game is that the best solution be the one that affects leagues rather than NTs. I said it earlier, but it bears repeating I think that the game would be better served by having similar sized leagues. I don't see the point of creating new small leagues from many micros.