Mostly just timing. Originally they didn't think they could get Sigourney Weaver back. She was too famous by then and hadn't been interested in making Aliens until they gave her a fat paycheck. Fox assumed she was done with the franchise, which is why early versions of Alien 3 (including the first treatments by Neuromancer author William Gibson) either didn't feature Ripley at all, or in a tiny cameo.

But, eventually Weaver relented and agreed to be in the film, but by then, Michael Biehn (Hicks) was booked solid for 2 years, including in the timeframe where they wanted film Alien 3 with Weaver. Hicks was the central character in the William Gibson Alien III (and does his own voice alongside Lance Henriksen in the fairly-good audio drama adaptation released a few years back). But his character wasn't considered essential to Fox, so they went with a script that didn't utilize Hicks, which was essentially a mashup of ideas from previous iterations, mostly Vincent Ward's version, only moved from a weird wooden planet (yeah, who knows) to a prison, and Ward's monks turned into a religious cult of prisoners. I'm assuming they just decided it was too hard to get from Aliens to an Alien 3 set on a prison planet without just killing off Newt and Hicks.