I can't really say that A:R's problem was that they got a "horror" guy. Whedon is known for action and snappy dialogue. (I would say wit and humour, but not straight out comedy.), and Jean Pierre Jeunet is known for... Well, much lighter material than the Alien franchise. It's been said repeatedly that even he didn't think he was the right choice for the job. I can't really fault him too much, i'm not too fond of his camera work in A:R, though. Lots of the fast moving zooms and stuff really make things look cheaper than they should. Just something about that style of camera work that has never appealed to me.
My big problem is I want these movies to be serious again. Prometheus and Predators both were fairly good turns in that direction, but Prometheus had some of that modern "Hollywood" type overly witty for-the-audience dialogue that breaks great movies. The original Alien honestly feels like a movie that does not even know it's own audience is there. Like we are literally looking through a rip in space-time into another world and watching things unfold. None of the characters are winking at the audience. I'm not saying turn the series into something pretentious. Just be straight. That's my biggest beef with A:R. Next to the other three it just feels like some kind of wacky off-the-wall comic film. Just in the way that it's shot and edited. The trilogy actually feel fairly consistent tonally. The Alien universe, at least in the frontier regions, is very unforgiving and oppressive.