Indeed, flying into some of the outlying Islands is pricier than others, but I'm not sure that there's anything much we can do about it.
Booking a return ticket to a single destination helps, eg flying in and out of Guadaloupe, say, you can get on charter flights that may save you money. Our preference is to fly into one area and fly out of another, avoiding a circular route during our weeks on the boat.
We have used the Island hopper flights such as LIAT or Caribbean Star but even those flights can get expensive (though friend last year found, on the net, a flight from Grenada to St Lucia for around $20 US/person.) They arranged round trip tickets to St Lucia and then sailed to Grenada and hopped back.
This last trip we flew into Martinique via American Airlines and American Eagle, and flew out from Grenada with the same providers and it worked out well, but cost for 4 from Vancouver Canada was around $6500CDN (incl. insurance) - not exactly cheap. But after searching all the travel sites and getting confused we used a trusted travel agent and I don't think we would have done much better. We were also very limited in our travel time options so that made things more difficult.
If your itinerary can be flexible you can probably do better too.
Good luck - adding the cost of the charter to high airfares makes the whole package a bit less attractive, doesn't it?