We sailed from Fajardo for the first time last December and really enjoyed it. Our trip was a bit different in that we were on more of a mission to spend some time in the BVIs as well as the USVI and SVIs. It was a fun adventure but I think next time we'd limit our itinerary to the USVI and not worry about the BVIs. We were fortunate in that there was no wind or swell on our trip East - though plenty of rain and even some lightning and thunder. There was substantial wind and swell on our return which although made for fun downwind sailing, I'm glad we didn't have to beat into those conditions. I think part of your route might boil down to wind direction and sea conditions at the time. If you get a primarily East wind, it might make sense to do Vieques first and then head to St. Thomas from there. More than a hint of North or South though (which is likely) and you might as well head straight East.

BTW, you may already be aware of this, but you are required to check in with customs when returning from the USVI to Puerto Rico (including Vieques and Culebra) by boat. Technically I think you are supposed to physically appear, but we were able to call in and provide the information. This is only when returning to Puerto Rico and not required for the trip West. They are quite serious about this and we received a stern warning for not clearing when we were supposed to. Here is the US Customs website that discusses it: http://www.cbp.gov/travel/pleasure-boats-private-flyers/pleasure-boat-locations/pr-us-vi.

Have fun - wish I was heading down with you.