Pecan Park IS going to hear flight pattern take offs and landings. I am fairly sure Flamingo will as well. Pecan Park was built to accomodate those HUGE in season flea markets while Flamingo encircles a small lake and most certainly will have better security. Either way, you are going to drive short distances to restuarants and shopping.
Me, I'd choose Flamingo. Have several retired camping buddies who live in Jax and they LOVE the place for small rally get togethers. Very personal service and care.
BUT, that's just me. There are plenty of boon dockers and Walmart lot campers on this forum and each of us selects within their comfort zone. Do what makes your experience all you wish it to be.
Be safe in 2013 and enjoy!