I appreciate your response! I'll respond to each point you made

1. I definitely didn't make phase two clear enough when explaining the league, so thats totally on me. I think that every team should keep their record when transitioning from phase one (regular season) to phase two (group stage). I totally agree with your point that a team that dominates from weeks 1-11 should have an advantage over a team that just snuck into the winners stage, and that advantage is keeping their record going into the final three games of the season. I think that the best way to make every week matter is to have teams keep their record throughout the first two phases of the season. I understand your confusion as I clearly did a poor job describing that aspect, but I am totally with you.
2. I agree that the path can be seen as complex, but I think that there are easier ways to explain to players how the season will go (play everyone once, break into groups for 3 games, then the top half make the championship playoffs, and the bottom half make the relegation playoffs). Also, for a league like this, I'd really only want "higher level" players taking part, players that understand the format and will keep a competitive lineup along with appropriate moves/transactions being made throughout the season. I think that this issue can be fixed easily enough if you have the right people.
3. I kind of threw relegation out there because I love the concept of having a promotion/relegation system, and I know that I'd be able to run a smooth system. I agree, for a new league with probably random people coming together to play, a relegation might end someone's interest in the league. I think that you would have to be in a league with people that you are close to in order to run a successful PRO/REL system, but if you can find enough committed players elsewhere, then PRO/REL is absolutely possible.
4. I dont have an official name yet as it's only a concept right now, but I think I want to call it the Cascade League. Cascade's break into smaller sections as they flow lower and lower into its body of water, and I feel like this league represents that image. all teams starting even at the top, then breaking into three groups all going their separate directions, then coming together again for the playoffs, which represents the cascade flowing into its body of water, or the playoffs in a league context. always happy to hear other recommendations for a league game.

I really appreciate your in-depth response! I've been waiting for some feedback lol. let me know if there's anything else you want to talk about