Here's my take on this. Nobody ever actually "sees" the Jedi spirits -- Force-sensitive people like Luke just feel them through the Force. BUT, you need some way of representing that on film, so you make the spirits visible. Now, prior to the scene in question (in the episode 1-6 continuity), we have never really seen Sebastian Shaw as Anakin -- even during Vader's unmasking, Sebastian Shaw's scarred face does not resemble his spirit visage at all. Since we are more familiar with seeing Hayden Christiansen as Anakin (having seen the six films in order), we are more likely to recognize him than Sebastian Shaw. (I remember that, as a kid, I was so confused as to who the third spirit was, since I'd never seen him before.) But that's just a way to represent the invisible spirits on film, so it doesn't really matter.

If you have a problem with Anakin taking his younger form again, consider this -- why didn't you have a problem with him as a fine-looking (albeit old) man, instead of a badly burned and scarred figure?