Personalized Partial Rejection...

Ah, sadness. I did a rewrite according to an agent's suggestions and sent them the partial. I got the rejection back today. It was a very nice, rejection though. I'd love to work with this agent. She said, "While I do think the new narrating strategy enlivens these pages, I'm sorry to say that ultimately I didn't feel the writing here to be quite mature/polished enough at this time." She also said, "I encourage you to continue to write and hone your craft. I do see the seed of a great project here and wish all the best in realizing your goals for it." That's pretty cool that an agent sees potential in me and my project.

I plan on querying her for my next project, for sure, if I don't get an agent.

Is it good manners to reply with thanks to someone who gives you a personal rejection, or is it just seen as an annoyance?

I sent her a thank you. Hopefully, in the future, if I query with another project, she'll remember me in a positive light.