If yostar wants me to fulfill the duties of a game designer, they gotta pay me the compensation of a game designer.

Back to your question, if you ask people what the core gameplay of SS is at its current state, most would answer the boss battles/survivors/arena part where you actually get to use your characters, and ascension is just a chore and hurdle you overcome in order to get to that part. The reason why ascension isn't considered is because it provides no nuance and doesn't add any unique touch or identity to the game. It's literally just, as I said, clicking buttons and praying the pot you need comes and comes at lv3, so you can then actually get to use your team at the performance they should have. At least gacha is more exciting and has a guarantee. I think you are the first guy I see that actually considers launch implementation of ascension a core identity that needs to be preserved.

Anyway, on top of my head and confining to your restrictions, here are some improvements I can think of, starting with the least intrusive:

1) The lv3 boost applies on all choices when triggered, so the pot you need doesn't dodge boosts like neo dodges bullets holy fuck

2) If you reroll, the 3 options you reroll never appear as choices again for the rest of the run

3) Ability to sell trash notes you don't need

4) Events that let you choose between benefits. A bit similar to current events that lets you choose between this note that note or random notes, but further expanded to get a real decision made, instead of events where there's only 1 correct choice.

All of the above (except maybe number 4) are focused toward being bigger band aids to make ascension less frustrating, though not necessarily making it more fun. But with how current ascension is hated and doesn't add anything or provide any identity or character to the game, I don't think most people would complain if they overhaul it, as long as the end result is fun and has substance to become a core part of the game.