It's not great like the two before it, but Alien 3 is still a good movie. Honestly, if it had been named something else, with different characters, it could've become a bit of a cult classic (kind of like how Darkman is, but, if it had been reconfigured as a sequel to Burton's Batman, it'd probably be hated). It's just that, being an Alien movie, people (myself included) expected it to be excellent like the first two movies and it was a full tier below them. Being much darker and killing off popular characters was initially disappointing, but, over time, one can start to appreciate that, because of it, it's actually (or, at least, tries to be) a deeper movie than either of the two before it. It may've missed the mark a bit, but how many other third movies in a series even take the risk and try that, especially nowadays?
I agree with this. It isn't that bad sequels can "ruin" movies--that's silly--but they can harm your enjoyment of the original. It's like how something that's been successfully parodied to death makes it hard to go back and enjoy the original. For example, if you're seen the Scary Movie series, it's harder to go back and watch certain horror movies like Scream seriously, since the parody bits creep in from your memory while watching. It doesn't have to be a conscientious parody, though. As movie series go on, they usually can't help but start to parody themselves by trying to outdo or avoid what was done before. They often just end up making a mockery of the original premise, so that it's harder to go back and watch the original without noticing the flaws in its premise.