How about putting Treasure on islands, which can only be gained by invading the islands with troops?  The Treasure could be olives, honor medals, credits, points or rescued prisoners/hostages (special sailors).  This could be chosen by the programmers and how the reward is divided by the fleet.  This would provide an incentive to use APA's for their true purpose and for using paratroops at a lower level than Harbour Attack and a disincentive to players just to shell everything.