Tournament/League Format:
This is the trickiest part of the whole thing, creating a format that works fairly for everyone, is smooth and quick enough to appease everyone aswell. I think that there is just a couple key things to consider. The size of the scene limits the amount of complexity you can introduce without making it unnecessary or have it function properly. The league format that the WNL used / NASTe used are great for larger tournaments with a larger pool of top teir teams being able to duke it out for a top spot. The picking system also allows for better match-ups and higher quality streams for much more intense and interesting play, however is the NA scene large enough for it? The alternative is the round-robin, however it has its own problems. A RR is great for smaller amounts of teams, however with the amount currently in the UNAC, it drags the tournament into months of matches with a lot of poor match-ups. I also dis-agree with two concurrent RRs, since there will still be a problem with poor match-ups, as well as making it a bit harder for the lower teir teams to improve over time and be paired with equals, while if we were to keep the finals bracket afterwards, it would just end the same with the same top-teir teams making it through, essentially just shortening the tournament, rather than improving it. (Though I suppose that is a small improvement itself

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Looking at the number of teams currently playing with the number of teams that can possibly be lost, and added, I would think trying at the NASTe or WNL style formats could work. NA kinda straddles the line between having enough numbers to keep it interesting, and having a Round Robin work effectively. Looking at the current season of UNAC, I think that it can be well worth the effort in attempting to change.
There are two issues that need to be adressed with this method, firstly being that of teams playing each-other too often, and teams leaving and entering. I think with the stability of the NA scene, with the size of the core clans playing, It wouldn't be an issue with either, as long as the rule-set is effect at keeping teams choosing different opponents each week, and having there be a good way to measure the standing, and honestly the current method of doing so works, and translates directly over to other formats.
I think if anything, there should be two season ending brackets, with the top 1-6 in a final, and 7-12/ 7-10 in a final, with the top two of each (6 teams) being seeded.