Once an agent has offered you representation should you expect to do editing? Absolutely. But wait, you say, if they want to represent my book doesn't that mean they love it as is? Yes, and no. Certainly they love it and feel as if they can sell it, or they wouldn't have offered in the first place. However, that doesn't mean they won't want to polish it up a bit. After all, they know how to make your work shine just right to catch the eye of a publishing house. Finding and polishing literary gems is what they do.
But how much should you agree to change at this early stage in the game? That all comes down to choosing your battles and realizing what's best for your story. If you missed cutting any of the fat your agent will find it and most likely recommend cutting it. A hint to catching more of it during your own editing is to look for any and all excess or unnecessary words such as 'that', and too many verbs. Those are things you shouldn't stress over cutting.
So why choose your battles, why not stand up for your book as a whole to protect its integrity? The main reason is because you want the agent to want to work with you again. If you're difficult to work with at every turn there is a good chance they'll drop you after the one book. If you only plan on writing one book that may not be such a problem, but for those of you who plan on writing another (or already have) you must choose your battles.
After cutting the fat (trust me, it's a huge blessing for you and the agent if they don't have to do that part!), then they'll get down to the story. They'll look for anything that doesn't flow or isn't integral to the plot of the story. If they suggest it doesn't flow they're probably right and you should seriously consider either cutting anything like that or changing it so it does flow. A break in the flow is not a good thing. If they want you to cut something they don't think seems integral to the plot, its time to sit down and rethink that scene. Is it integral? Will it tie into a second or third book down the line? If so, explain why and fight to keep it. You may be asked to get rid of non essential characters. I had a character in one of my books that died only a few chapters in. While I liked him, he didn't really add anything important to the book so when my agent suggested I cut him completely, I did. However, if I had plans for him to reappear in a follow up book, I would have fought to keep him.
Aside from wanting to work with your agent again, there is a secondary reason you want to choose your battles. When an editor picks you up chances are they may ask your agent how you are to work with. If there is any chance your story needs much work at this point in the game you really want that answer to be a positive one or the agent may pass.
Take a good hard look at your agent's critique. Understand that they have your book's success in mind. Stand up for what is necessary and be ready to let go of what isn't.