I love both Bubba Gumps and Margaritaville, but I can't really choose one of the other.
Bubba's has great shrimp dishes, but if you don't like seafood, stick to Jimmy's because Bubba's is mostly (if not ALL) shrimp, and their non-shrimp items aren't that great (I once unwisely ordered a chicken dish their to have it come out dry. They do have nice special non-alcoholic drinks like the straberry and blueberry lemonades (which kids will get a kick out of), and their Runnin Across America appatizer is great for a single meal (as well as gives you a variety of choices when you can't pick ONE of their tasty meals), but if you don't like shrimp, I'd avoid it.
Jimmy Buffet's is a fun place for kids and adults to wind down and let loose and is a great atmosphere for kids (balloon hats, huge servings, sing-alongs). But...if you want to eat there, get a reservation. We usually stay on property, so the wait's not that bad, but it can be an hour to a two hour wait....sometimes more. And it's also a popular place for companies to reserve for parties (we once tried to go their on our last vacation, and had to reschedule for the enxt night do to it being booked for a special party). Food's good there, but I'd try to make reservations in advance and make sure no private parties book it the day you want to go.
Overall, they have their pros and cons: both have good food and service (least everytime I go), but it's your choice. Hopefully this helps.