Dawson Casting: Nicely averted by the actors who played Catalina, Bova, and Rosie, all of whom were 13-14 during the first season. Radu and Suzee were borderline; both actors were 19-20 during the second season. Played deadly straight with Walter Emanuel Jones who, several years earlier, had been too old for his role in Mighty Morphin' Power Rangers and, well, hadn't gotten any younger since.
The original season 1 finale came without the tacked on ending where it is revealed Catalina survived the explosion in another dimension but Nickelodeon demanded they put it in because children can't handle death. Also, it was originally planned for Elmira to officially join the main cast in season 2. However, Nick executives felt she was too "alien" and were afraid fans would find her scary. So, they replaced her with Susie.
Other examples of Nick's meddling was moving Davenport and Goddard into the background in season 2.
What Could Have Been: As mentioned before, at the end of season 1, the intention was to have Catalina stay dead, and have Elmira take her place on the Christa. However, Nickelodeon squashed both parts of that, saying that 1) children wouldn't be emotionally capable enough to comprehend a character death and 2) Elmira was too alien. Thus Catalina's death was rewritten as being pushed into another dimension, and Elmira was written out and Suzee was written in.
On his website, Peter David went over numerous ideas for the series finale of Space Cases, including crossovers with both Lost in Space and Babylon 5. Nickelodeon executives refused outright, claiming kids wouldn't be familiar with either.