You don't have to listen to anyone else when they suggest changes to your story.
When I first began writing, I was assured by other aspiring authors that I should always do whatever I thought best for the story. That others were welcome to provide suggestions, but that I didn't have to take them.
If you want to get published, you don't rely solely on your own opinion.
As I've surfed through the many, um, interesting works on authonomy, I've read many rants from potential authors, where they've adamantly refused to change anything about their writing.
I can only imagine how agents feel when they've spent hours reading a manuscript and making suggestions, only to hear that the author didn't agree. Yes, it's our perogative not to change our own work, but did we actually try implementing those suggestions? Almost every time I've gotten feedback from an agent or editor, I've tried it out and discovered it made me sound much more brilliant than I really am.
An author friend of mine (3 published works) always advises me to make the changes agents/editors tell me to make. Yes, it stings to know my manuscript isn't perfect, but if I take a day or two to think about it, I almost always end up agreeing with the suggestions.
What do you think about making changes based on agent's/editor critique?