The Mel arc is the easiest fix I can see off the top, as far as season-long plot lines go.
Her mage thing added nothing to the story that couldn’t have been introduced via Ambessa, and Ambessa’s own motivations would have been much more convincing had Mel been killed at the end of season 1. Even her “courting” of Caitlyn would have been much better if they had been able to connect over the shared demise of a loved one at the hands of Jinx.
Edit: Noxus’ moves to infiltrate Zaun would have also had way more plausible deniability if one of their prominent diplomats had been killed by a “terrorist attack.” As it occurred, I’m not sure why Piltover would have believed that it was anything other than an opportunistic play at an eventual hostile takeover.