A lot of movies like that are products of their times. Breaking conventions, introducing new technologies, etc., gives them an edge because it's new and different, so the experience overall already has that going for it. If the story, script, and acting are at least good, you've got a hit. Unfortunately, it's easy to look back on those same films and wonder what the fuss was all about. I thought Nightmare was a weird (it is Tim Burton after all) but also very different and cool. A twisted take on some widely-held mythology that no one really believes, but it's fun to buy into the lore just long enough to see it dissected.
Roger Rabbit is the same. The interplay between live action and traditional animation is brilliant. The story is weird, but holds together long enough to get you there. The real star is the novelty of the movie itself, combining WB and Disney cartoon characters with live action.