to have such a dilema! You can't go wrong any way you choose!
If you want white silky sandy beaches with turquoise waters, good snorkeling and shopping then i would go the Eastern Route.
The Western Route is a bit more active with things like swiming with the Sting Rays,climbing water falls, river tubing, zip lines, awesome snorkeling, Mayan ruins and really nice beaches.
The Southern Route is your most port-intensive route, this is the route that will give you the most exposure to local towns and the local island flavor, you will find lots to do and great beaches to explore.
Since you will be traveling during the peak of hurrican season,and if airfare to San Juan is not a concern i would lean more towards the Southern route - these islands are out of the hurricane belt.