I think it's not a matter of who writes it, but what it is they are offering to the franchise.
Let's take the Alien franchise, for example. This first film turns what people expected of a horror flick around. Every time they expect something to happen, something different happens. When they expect a character to die, they are fooled until finally they actually bite it. It's a classic film and arguably the best of the series.
Then James Cameron comes along what...six years later? Maybe even more? And he decides "hey, let's have MULTIPLE aliens this time!" Only he does more than that. While the main draw is "guess what? This time there's marines fighting aliens!", there's also a lot of depth added into the universe. "The Company" is given a name and purpose: Weyland Yutani. In the director's cut, we discover that Ripley had a daughter back home, but now she is dead. This adds to her relationship with Newt, who has lost her entire family. Androids have been changed, but due to Ripley's previous experience her character has difficulty trusting Bishop. So on and so forth.
In other words, the Aliens franchise not only promised the untrustworthy "BIGGER AND MORE BAD ASS!" exclamations, but also provided more depth to the universe. Even Predator 2 managed to delve into the culture more. It's not only non-combatants that the Predator doesn't face, but pregnant women as well. There's a shit ton more weaponry. At the end, we discover that the Predators have been coming since the Revolutionary War and probably even earlier than that. Plus, if you defeat a Predator, then you are no longer prey but instead accepted into one of their own (all of this added depth is, ultimately, why I prefer Predator 2 over the first film, despite "worse acting" and a "lame story"....even though the first wasn't that great in those departments either).
Alien 3 is debatable. It was demanded by Fox so they could make more money, and it didn't add to the universe in any way. It was, overall, pointless. However, it still remains my favorite because the the director, David Fincher, took the script and got some writers to help turn it into something much more interesting. The movie is now about Ripley becoming her own worst enemy, and she is now in a situation the other films hadn't tackled: a woman alone in a prison of Double-Y chromosome males that have found God and are struggling with redemption. Sure, it's back to one Alien, but at least they defeated it in a different manner than tossing it out into space. Ripley's death was also intended to put a definite end on the series so Fox couldn't clamor for more cash.
Too bad. They got Joss Whedon, a fan, to write another script, and his was better than what the asshole French director did to it (why would you get a romantic artistic director to tackle an Aliens film?), but it added nothing to the franchise. It merely played with what we knew of the universe and revived Ripley.
There is nothing wrong with fans writing a sequel, as James Cameron was clearly a fan of Alien but managed to make a fantastic follow-up that expanded the universe. There is also nothing wrong with a company trying to milk a franchise if the right person is put in charge (Alien 3 is not the best, but as a film it IS good and continues to be my favorite, but if you won't accept that then I present the old kid's show Mighty Max. A guy was told to create a show for a new line of toys, and instead of creating a mere commercial the guy created an entire universe that explored all kinds of cultures, ancient legends and paranormal theory. It was also the first kids cartoon to actually have people die since I watched Robotech, which was bad ass).
I think the biggest problem isn't necessarily a fault of fans. It is people trying to make a sequel without having a purpose. James Cameron had a purpose in returning to the Aliens franchise, and it shows. David Fincher created a purpose, albeit a rather weak one (then again, that's what happens when Fox demands a sequel). No purpose, and it'll just be absolutely worthless as a game or film.
Interestingly enough, I couldn't play through the first F.E.A.R. game. I found it rather...boring? I dunno. I think I didn't like how it controlled or something, but overall despite having some cool ideas it never grabbed me. I really enjoyed F.E.A.R. 2 though, even if the story was...well, it was there.