You're not alone with that, the endings are the problem of a lot of the games here.
On the other hand, there are many games that should finally come to an end, but still artificially kept alive by endlessly dragging the story.
Finding the right time and the right point to end the story is an art of its own.
Yes. The prologue conveys a completely different game than what it became.
To clear things up, it might be better to integrate the Ellie content from the prologue into the main game and discard the rest of the prologue - all the other Li's don't appear later anyway.
As it is now, it is really confusing and that was one of the main reasons for the criticism that came up here.
I think your problem was, that at the beginning (the prologue time) you didn't even know for yourself, where you were going with your story.