I've stayed at a Hampton Inn and a Courtyard Marriott at the Jax airport exit. Both were fine (nothing special) and pretty much what you'd expect for those chains. I also stayed at a Holiday Inn that could use some updating and was filled with all the airline employeess. Beware, however, of the airport exit in general though. I saw some sketchy looking motels there. Can't remember the exact brands, but they were the chains that are one step down from Hampton (Days, Quality, etc.). If I'm remembering right there were also two Comfort Inn and one looked nice/new and one looked scary.
If you can make it to the southside of Jacksonville, there are much nicer places to stay and more choices for eating. Check out usastar.com/lodging if you haven't already and it will list what's off those exits. It might also be nice to get through the Jacksonville traffic (still construction there as well as past there to nearly Daytona) if you're not arriving at evening rush. If you decide to go north of Jacksonville, I've heard there are some decent places in Kingsland, GA, but I've never stayed there.