Not really, as far as I know they're pretty much the same. Just the red sea is newer and more modern looking. The red sea is larger(34g right?), if so, if you are new it would be a little easier to keep water tempraments in check as it takes longer for them to change in larger volumes of water, but 6g isnt much of a difference.
I've only talked to a few people with the red sea, but know a lot with the JBJ and they're really satisfied.
It's really up to you, go with the one you like best. But the good thing about buying a cheaper aquarium, you'll have the money to upgrade stuff that could have been crappy on both, whereas with the pricey one, you might not be able to replace stuff right away.
here is a site that compared them:
http://www.nano-reef.com/forums/index.p ... 8644&st=20
hth, Josh