I agree that Anakin, in theory, should have been almost unrecognizable. The burns he suffered would have left his face a melted, scarred, horriffic mess to behold. But, I'm pretty sure they pulled back on his appearance in ROTJ because they wanted you to seeAnakin. There had to be some payoff. You wanted to get some sense of who he was and what he looked like. They needed to reveal a human being that the audience could relate to. Had he just looked like some melted ball of wax, it would simply have been yet another mask that gave no real indication of who Anakin was, so they pulled back the make-up so as to show us Anakin's face, while the surrounding scares implied that something horrible had happened to him.

On a related note, one other thing I hate about ROTS is how Anakin's trademark scars about his head and face just suddenly materialize with no apparent reason. Those aren't burn marks, they're deep cuts, and impact wounds. For all the thought that went into the make-up, the wounds should have made more sense.