I agree with Viddiest! (Also, congrats on the R&R. Agents don't hand those out, unless they really do see potential for the novel and like big parts of it). If you connect with the suggested changes, and you like your new manuscript better (ie, think it's stronger), then by all means, keep the revisions! You should only throw out the agent's comments if they don't sit right with you, or it's not the direction you want the novel to take. Agents will have different visions for novels than authors sometimes do, and it doesn't make anyone wrong. You just have to know if you agree with the vision. And in the end, you're the one who calls the shots about what vision to follow.
I got a R&R a few months ago from an agent, and upon reading her comments, couldn't believe I hadn't already made those changes. Everything made sense with where I wanted to take my book, and I felt that she really saw the core of it. So I decided to revise. After 3 months of extensive revisions, I had a manuscript that I loved even more, and knew was much stronger.
Best of luck!