Well since Disney bought Marvel and Howard The Duck is a character owned by them. Maybe we'll see a new Howard The Duck movie in the same vein as Roger Rabbit sometime.
"Listen, do you smell something?" Ray Stanz-Ghostbusters
This is actually a pretty good idea! Disney has teamed up with Marvel, so this would be the perfect project! Could you imagine? The tagline could be "Move over, Donald! There's a new Duck at Disney!" And the poster could have Howard pushing a picture of a mad Donald with his fists balled up ready to fight to the side! This time, it shouldn't have so much crude humor, (just a little subtle crude humor) so it could appeal to a wider audience. That's sort of how the original failed. Audiences didn't know whether it was an adult or children's movie. So, they should sort of make it a family movie. But it has to have a good story, which most Disney movies have. A good story could be Howard and Beverly being transported back to Duckworld, somehow, only to find it being destroyed by Dark Overlords. Then, Howard, Beverly and a rebel team of ducks team together and fight back, with flying battleships! I saw a fan-made trailer on Youtube with this storyline with the title "Return to Duckworld", and thought that would be pretty awesome!
Also, to the OP; when you said they could do it in the vein of Roger Rabbit, I do think the two movies are kind of similar. They are both wacky take-offs on the noir genre, involve a woman's weird relationship with an animal, and that bit of music from the beginning sounds a little bit like a piece of music in Roger Rabbit; (just watch the scene where the camera pans across Eddie Valiant's office)