I think the biggest issue was that everything felt rushed and the character arcs weren't given enough time to breathe. They didn't even succeed in entirely connecting the plot to LoL lore.

If the objective was for the characters to end as their in-game versions, keep Cait being bloodthirsty. She loses her moral integrity and compassion for the people of Zaun and is blinded by hatred at what she perceives is the place that took her mother.

Make Vi and Cait fight for longer. Vi is from Zaun, she wouldn't become an enforcer overnight and abandon years of hating them so quickly. Separate them and spend time actually showing Vis' struggle instead of shoving her in a montage.

Make Jinx even more insane. The point of the climax of season 1 is that she abandoned Powder and fully embraced becoming Jinx. Make her go off the deep end instead of trying to redeem her. Her insane actions will be what pushes Vi to fight against her and join Caitlyn eventually. I liked that she became a revolutionary icon for Zaun, keep that.

Ngl I do not like the Viktor storyline. It completely loses the essence of what Arcane was about. But if we recontextualize it as "Piltover and Zaun are both under threat from an outside force" it could still work. Making Viktor and Ambessa work together was the correct move, it makes sense for their characters and pushes Piltover and Zaun to fight against a common enemy. The difference would be that they are fighting separately, not shown to stand as a united front. Perhaps Zaun takes advantage of the chaos of the Noxian invasion to try to take over Piltover or force their hand.

After Ambessa and Viktor are defeated, THEN is where the Vi vs Jinx fight happens. Despite having fought a common enemy, they cannot reconcile their differences, and by this point Vi would be more enforcer-pilled and would want Jinx to answer for her crimes. Neither of them really win, and Zaun retreats from Piltover. After the Noxian invasion, Piltover doesn't have the resources to keep control of the Undercity anymore, so it declares independence.

You could honestly probably do away with the Noxus and Viktor storylines or reestructure them into something better, but I tried to accommodate them as best I could. With this reframing, the themes remain the class struggle represented through the two sisters; a tired underclass revolting against their oppressors, the oppressors moving to more and more authoritarian means to keep control (Caitlyn's dictatorship) and even class traitors (Vi). And you also set up the characters to be like their ingame counterparts. Though honestly I think it's best if it keeps being an alternate universe, but whatever.