Honestly, I think Daisy works pretty well in the plot as-is, once you hit certain revelations near the start of Act 3. 'Who do you dream of at night?' works much better in that context than 'You need a guardian.'
The Wyll changes are really unfortunate. I didn't like him much in EA but it's like Larian rewrote him to remove his ambiguity and bring all of his 'big moments' forward (in EA, didn't he say Mizora was his human lover?) and there's just nothing to replace it with. The Guardian stuff I can ultimately take or leave, but the Wyll changes are bad. Especially tying him into Karlach -- just who is going to kill Karlach, one of the best characters, for Wyll? You don't even have to roll or anything to talk Wyll out of it.