I really would have liked the ability to confront Alphys after MTT spills the beans.
Honestly I think the Alphys section is the weakest part of the game, there's no variation in how she interacts with you regardless of if you're going on a killing spree or not, no response if you've killed Undyne, etc.
I didn't dislike the content that was there, mind you, it was just a lot more linearly scripted than the rest of the game.