Well if they changed the itinerary after you booked, did you try and call and ask them if they would/could change you to another ship that does include San Juan? Since they made the change they may do it without charging you additional fees. Of course they may not too, but still worth a try.
Now having said that, the other problem with San Juan is that the distance from Florida makes it a problem from the standpoint of the time you get there. A normal cruise won't dock until 3PM if SJ is the first stop. This makes the tours that can be offered limited. This may be why many cruisers do not enjoy stopping there as much as other ports. The only choices seem to be going out and having dinner.
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise, Magic 1/14, Freedom x 2 6/14
NCL Dream October 2006, RCCL Mariner OTS June 2007, Celebrity Silhouette 2013