I really like my Yakima roof rack system on my Toyota Highlander -- no trailer to store.
Invest in a leash for your Mirage drive -- you'd hate to have a mishap and the drive end up on the bottom of the bay.
I have a Scotty flushmount rod holder on each board -- they work great.
Get a good dry box for your keys, wallet and phone.
Fishing on the Bay, you might consider a drift chute.
The Visicarbon light looks very cool. I bought a flag and a suction cup light from my dealer, which are fine, but the suction cup on the light won't actually stick anywhere on the PA. I had to cut a disc of clear plastic from the light packaging and glue it to the top of the front hatch to have a suitable mounting location for the light. The Visicarbon appears to give you the light and flag all in one unit.
The Hobie inflatable lumbar support isn't pictured in the catalog, but it is listed in teh detailed parts listing. Check with your dealer as they may have them in stock. I have trouble with my lower back, and this inflatable support is a life saver. It really helps make the seat more comfortable for a long day on the warer. It attaches to the seat with a strap and has an inflation nozzle that makes for quick and easy pressure adjustments.
It's not cheap, but if you want to memorialize your trips with good pictures, think about a waterproof camera and mount. I liked the looks of this camera with a remote control that I tried at Bass Pro Shops http://www.kodakoutdoors.com/playsport-video-camera-bundle
and this kayak camera mount http://www.xshotpix.com/kayakmount.php
, but the price tag is a killer.
In the end, except for the things to protect your life and equipment, most of the other items are just nice to have stuff. The best suggestion I have is to get on the water, often! You're going to love it.