That's a bit difficult to describe. Every film has its own dynamic, its own rules. Cronenberg's Fly has rules of its own (in terms of tone, characterization, etc.). The film's fictional science also has rules (based, for the most part, on real science concepts like gene-splicing, etc.). The Fly II's science fiction concepts (gene-swapping, Martin's cocoon metamorposis, etc.) don't jive with the rules established about the Telepods and the mutations (or, in the case of the cocoon, insect biology) seen in the first film (Indeed, in Cronenberg's film, the Telepods destroy objects and recreate them from raw stock--in a draft of the Fly II's script, it is stated that the pods work much the way the booths in the 1958 Fly film work: by transmitting atoms like a tv signal).
Then there are some continuity issues and flaws in logic:
In the first film, Bartok Science Industries funded Brundle's work, and was made to sound like a relatively small company. In Fly II, the sprawling company is called Bartok Industries (minus the "Science"), and is evil! I can't believe Seth Brundle would have worked for someone as obviously evil as Anton Bartok!
Also, we have the replacement of Geena Davis with Saffron Henderson (Are we to assume that, retroactively, Henderson played Ronnie in the first film? Henderson plays Ronnie in the birth scene, and overdubbed Davis' dialogue for the first "Seth Brundle videotape" sequence--actually a deleted scene from the first film). It is hinted at that Ronnie was taken in by Bartok and tricked into giving birth to Brundle's baby (he presumably told her it would be normal), whereas in Cronenberg's version of events (the first film's deleted epilogue/epilogues), Ronnie either aborted Brundle's child and got back together with Stathis, or decided to have the baby (without any sort of Bartok-interference). A logical extrapolation of Cronenberg's Fly universe would be that, after the events of the first film, telportation research would continue, but most likely without the sci-fi/horror aspects of the film (and would then change the world as we know it). As Cronenberg himself has said, Seth Brundle is akin to the first people working with radiation. Some died, yes, but the work progressed. Instead, Fly II gave us Bartok's master plan of using the pods to "control the form and function of all life on earth". Uhhhhh....wouldn't he just want to get filthy rich off having the patent to freakin' *teleportation*?????
And of course, the Telepods are structually different from the ones in the first film (which were destroyed and had to be rebuilt for the sequel), make different door/lock/teleportation sound effects, and for some reason don't work correctly at the beginning of Fly II (aside from Telepod 1 being severed from the computer and Telepod 2 being destroyed at the end of the first film, they worked fine).
And the second videotape of Seth Brundle that Martin watches (where he talks about his accident with the fly) should not exist. That was a private conversation from the first film between Seth and Ronnie that was not videotaped. The *only* way Bartok's people could get footage of that conversation...would be to go to the local video store and rent or buy first film!
But, as I've said, taken by itself, Fly II is a fun little gothic horror film, with a fine payoff at the end (we see Bartok pay for his evil deeds, and Martin--and perhaps, in a way, Seth--is redeemed.).
