I would remove masters and kick off events.

This would make champions more fun and valuable since its the only time in the year where all the teams from the world can compete.

Kind of how the football world cup works. If you have a world cup every year then the championship it's not worth that much anymore.

This would also allow for longer seasons in domestic leagues

Right now you have FRANCHISED teams that play less than 10 official matches a year. You can make a league where every team plays each other in a double round Robin, which would be the entire season, and have every team play at least 22 matches every year. This helps sponsors and long term projects.

I would also allow academies to ascend, but only if they choose so.
Let me explain. If you're an academy and you qualify for ascension, you can choose whether to play it or not. If you choose to play it and you win, your players can't go to your main team, you have to sell the spot including the players to another org. Maybe you can keep 1 player, I don't know, but this allow for more investment in tier 2.
If you choose not to play ascension then you can have your players just as it is now.