Way I see it, there's two distinct paths we can take from here.
Option 1 is a low risk venture, keeping the game schedule mostly as is (2 game week, 22 game season). We can still achieve the 13 week season that I've always vouched for, resulting in less downtime for everyone. It involves dropping the unpopular all-star break, and making the finals a single game because usually game 1 decides the series anyway. And I'm sure there's easy ways to tweak the cup, B3 and national tournaments so they fit a 12 game schedule.
Option 2 is a high risk, high reward overhaul, adopting a 3 game week system. This will be substantially harder, as the game shape mechanic in it's current form would have to be scrapped. A rolling fatigue system might be the answer, which would also encourage managers to run deeper rosters. We still need enough weeks in the season for the various cups, meaning that this would mandate a 30 game seasons, scrapping the conferences. Including the play-offs, a 12 week season is the result (my play-off format in this case would be four teams, two-game aggregate in both rounds).
I think one of these options should happen. Even if you want to keep things the way they are, there's always room for improvement within the way BuzzerBeater currently works.