The most important difference is that the Gecko is bigger than the screamer, in both feel and actual volume. However, the Gecko in its Ultra form was 600g lighter than the CGI Screamer, so it feels very light and throwabout underfoot for its size. It's the better light-wind/big-sails board, and our 95 kg tester was emphatic that it was the better heavyweights board, being easier to sail and turn.
So, for the lighter weight sailor, the Screamer is perhaps the better option. And whereas the Gecko is generally the better choice as a first time slalom board, the Screamer is a bit more throwabout and exciting, and thus better as a second/third time slalom board.
As for performance, there's very little in it. The Screamer feels a bit more clattery underfoot, and was perhaps a fraction quicker going out from the beach, but coming back in over the backs of swells and chop the higher nose of the Fanatic gave easier clearance. However, both have an excellent rocker profile for jumping and gybing. Both are extremely forgiving and versatile to gybe, and great boards for really getting to grips with the move.
Finally, for barefoot sailing enthusiasts, the Gecko seemed to have just slightly better nonslip than the Screamer...