Nothing Bad is Ever Whedon's Fault
Even the finest screenwriters shit the bed. It happens. William Goldman, Oscar winning mind behind Butch Cassidy and The Princess Bride, also wrote the adaptation for Dreamcatcher. Did he blame anyone else for that crap? Of course not, he's a pro.
Alien Resurrection is just as shitty. But that's not Joss's fault. According to him: "They said the lines ... mostly ... but they said them all wrong," he said, regarding his script for Alien 4: KY-Shitfest in Space, before going on to say, "They cast it wrong. And they designed it wrong. And they scored it wrong. They did everything wrong that they could possibly do." So according to Joss, putting Michael Wincott, Ron Perlman, Brad Dourif, J.E. Freeman and Sigourney Weaver in your ALIEN movie is horrible casting. And the director, who also directed City of Lost Children, might as well be Helen Keller. But the writer, the guy who gave Ripley a robovag sidekick more annoying than C-3P0, and made the main villain a fucking Muppet Baby? You insult him in a dream, you better wake up and apologize.
Muppet Babies, they'll eat your fucking skull...