We just got back from our second trip to the BVIs so hopefully I can answer a few of your questions. First, the beaches on Anegada are gorgeous, but the day we were there (in late December) it was brutally windy - you couldn't lay out, or read a book, or really even hear yourself think. So I think it depends on what time of year you visit (it will obviously be windier in the winter). You will also definitely want to make sure that it's a nice day, since there is nothing to do there but eat lunch and go to the beach. The ferry ride from Tortola was 1.25 hours, but it passed quickly (we brought books). From VG it's about 45 minutes.
JVD and VG are both good choices. The Baths are truly spectacular (we've been twice and were still dumbfounded, even on our second visit!) and the party scene at White Bay/Soggy Dollar on JVD is a great way to spend a day. Be sure to ask your boat captain to take you to Sandy Spit off JVD - it's like a classic "desert island" that you won't want to miss!
Finally, Cane Garden Bay on Tortola is gorgeous, but you will want to check the cruise ship schedules before you go there - when the cruise ships are in, there can literally be thousands of people on that one beach. One neat thing to do on CGB is to visit Green VI, an open-air glass-blowing shop that sells gorgeous pieces of hand-blown glass made from recycled beer bottles collected from local restaurants. We spent the better part of a morning there watching them blow glass (they also offer classes) and admiring all the lovely pieces before deciding on which ones to take home.
Not sure when your trip is planned, but I will have a very long, photo-filled trip report ready in about a month that might be helpful to you as far as other things to do, where to eat, etc. It will be posted here, so be on the lookout! :)