First, congrats! An R&R is definitely better than a rejection!
My assumption is that the agent loves the first one but is not convinced about the other one or two. Agents don't make much $ with PBs and they like to know you are in it for a career, not just a one and done. So by giving you a revise/resubmit, they might be seeing if you have what it takes to take a good manuscript to a sellable manuscript in their eyes. And also to see how you take revision advice. Do you just make superficial changes or do you think about what they are asking and dig deep and revise.
It's also a way for you to see how you work with this agent. For the most part, it will be rare for you to send in a manuscript and not be asked to make any changes. Do you agree with the vision that the agent has? If not, how can you communicate that and still possibly find a way to make the PB better in both of your eyes? I actually think an R&R is a good way to "test" a relationship before you sign with an agent. She/he sees promise in your work, but it's not quite "there."
So my advice is don't rush this R&R. Think about the changes that you are being asked for. Revise, let sit a bit, and see if if feels right.
Best of luck!