Personally, the problem with Eliza is that her major choice doesn't come around till chapter 5 despite her being with you from the start. So if you want to tell her no, it's two chapters of telling her no over and over, then the chalice arc doesn't have much with her in it, you get bombarded with Kira instead. Chapter 4 is back to telling Eliza no, and you finally get a permanent no in chapter 5.
She should have been the first major choice and the fact she wasn't is a mistake. The only way I can justify it in my head is that Buu wasn't sure he was going to use the "major choice" system until later and didn't backtrack to toss one in for Eliza sooner.
On a somewhat related note, not liking the main girl of the game has to sour the overall experience, I'd imagine. Personally, I like Eliza but I've been playing this Pokémon style so MC is at best a womanizer.
"Sure, Eliza, babe, I love you, I just need to step out in the hall for a sec. Oh, hey Anna, wanna go down in the cellar and do that thing we did two updates ago again verbatim? Yeah? Okay, let's go. Bye Eliza, love you."
The island arc exacerbates this to unbelievable levels.