Nick,
The costs don't typically come into play, as you'll pay $9 to get through the cuaseway tolls, and probably pay the jet ski guy $20 to pull your trailer to the beach with his atv. Not a large difference in cost, and the jet ski guy is providing a service in my mind, so worth the extra $$$
I always park at the beach on the causeway, where I launch. However, this is the important part and please don't screw this up for the rest of us: Technically the park rules don't allow "launching" and they define this as backing your vehicle down into the water and "Launching" your boat off the trailer. To the park rangers, this causes driving to close to the beach and thus erosion. The goal of the park rule is mostly to force boaters to use either the Fort Myers ramp at the east end of the cuaseway, or the Sanibel Ramp at the west end. If a park ranger sees a jet ski at the beach, and sees a trailer attached to a vehicle, they will make them leave and park/pay at the boat ramp parking lot on either end.
HOWEVER, Kayakers, Windsurfers and the likes (Beachcats), get a pass since those vessels are walked/carried into the water and don't cause erosion and tyically would jam up the boat ramps for the boaters. So, you MUST use your beachwheels to walk your boat into the water. Trust me, i've had park rangers walk up to me and my parked vehicle with the trailer attached and they make sure that i'm not using the car to "launch".
As for which site to sail from, to me it depends on the conditions, etc. Fort Myers Beach can be a bear to get off of in the afternoon, as traffic really backs up leaving. But, the beach is much, much nicer, white sand and a good day to hang. The causeway is not a traffic issue, but its basically a shelly gritty beach, so you don't hang out there if not sailing.
If you were to launch from FMB and sail to sanibel its about a 5 mile distance accross.
Hope this helps.