As the 1986 film was so successful, plus the original had multiple sequels anyway, it shouldn't surprise anyone that a sequel was thrown together for the new imagining. However, "thrown together" may be a little more apt than one would like, considering science fiction movies how up in the air so much of the story was during pre production and the fact that (blog post) despite being a direct chronological sequel the two films could hardly be any more different.
Source: The Fly II Movie Review - Decker Shado