Sending a revised MS

I've never had an R&R, but I'd go for option number two - no harm in refreshing the agent's memory! That said, I'd keep it to one or two lines. If you want, you can always sum some parts up like, "[...] plus some other changes to speed up the pacing/deepen the romantic subplot/whatevs."

I also think you should include some info about the changes that you made, to refresh the agent's memory.

If you did something that they suggested I can see mentioning it so they know you took their comments to heart, but otherwise I don't know if you need to be all that detailed. They'll see what you did when they start reading. Pointing out past flaws feels too negative to me when you want to start with a fresh positive outlook. It just reminds them why they didn't like it the first time.

When I resubmitted after requested revisions (the agent had read a partial), I just mentioned that I'd addressed the areas of concern. I don't think that I even specifically referenced the items the agent had asked me to address, because I didn't want to bring up things that were obvious deficiencies to the agent in the first place. That seemed to work just fine, but I also resubmitted within about three weeks.

If you have a longer break in between first submission and sending in the revision, it might be good to mention what you've changed, but maybe phrase it like: I've addressed the areas you pointed out as concerns, while maintaining (insert items the agent seemed pleased with).