Why some people hate Lily so much? It's true that at the beginning can be annoying, but the reason for that is not only explained from her point of view - you left the town without contact and come back and act friendly like nothing happened - but it's even resolved. Plus you can see what effect this have with her in the "Lily Trust Bonus 01" on your pc, once you unlock it.
Lastly, her personality is good for the story of the game. Can you imagine all the character be the same? You should think, sometimes, that some developer want to create a story with some realistic interaction, instead of "oh, you are in the same class as me, let's frick".