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At the end of "Return of the Jedi" Anakin's head was replaced with the head of Hayden Christensen.

This question asks when this was done, but what were Lucas' reasons for doing this? All of the original Star Wars fans would surely be disappointed (as they were).

There is indeed proof that only the head on the ghost was changed, which makes it all the more ridiculous.

It seems that every time they release Star Wars on a new media they change something. Why doesn’t it stay the same?

Lucas had repeatedly stated that he has an artistic vision and all the changes are to make sure the movies are as close to it as he wishes. That's the one and only reason.

As far as Anakin's head, that one actually made sense. Darth Vader wasn't a Jedi, so it was pre-Darth Anakin's shape that would be the most natural for a Jedi's Force Ghost. That is how Anakin remembers/sees himself.

(Src: Wikipedia)

P.S. The following reasoning is listed on Yahoo Answers but I haven't found proper sourcing quote so it's suspect:

First, Lucas was trying to establish a "familiar face" to the character that would link the OT and the prequels together. If he had stopped there most "old school" fans would have still not liked it but would have let it slide ... BUT ... his second reason is asinine. He said that a Jedi's "Force Ghost" is the image the Jedi had of themselves when they died and that Anakin died when he became Darth Vader.

It's honestly pretty inexcusable, and there's (to my knowledge) no official reason for the change.

That said, I can sort of understand the reasoning behind Lucas's decision.

Put down the pitchforks and let me explain, people.

In the early 80s, they were writing and shooting Episode VI: RevengeReturn of the Jedi. The climax of the story was

The redemption of Anakin Skywalker, and the death of Darth Vader

Anakin, at that point, had been 'dead' (from a certain point of view) for 23 years (turned Sith in 19 BBY, died in 4 ABY.

Darth Vader was seen throughout the trilogy, large and menacing. He breathed heavily, dispassionately executed subordinates, and generally was a big bad nightmare.

In Episode V and VI, we learned that Anakin, the hero from the Clone Wars and amazing pilot, was

Darth Vader

Luke's quest changed from avenging his father (as part of saving the galaxy) to saving his father.

Still, at that point, the audience had never seen Darth Vader's real face. We briefly saw the back of his head (or part of it) in V, but it wasn't until after his redemption that we saw his natural human face.

The actor who played that face was thus used as the actor for the Force Ghost at the end, showing that Anakin had truly been redeemed. The audience may not have recognized him with hair and so much less makeup, but the connection was easy to make.

Post-Prequel Trilogy? We know what Anakin Skywalker, Jedi Knight (and General) looks like. We saw him grow from a podracing brat to a whiny, self-absorbed 'adult', to a hero. Anakin Skywalker isn't a plot device anymore, he isn't a figure of myth and shadow, he has a distinct, recognizable face. It's much easier for an audience in modern times, having watched all 6 movies, to connect Hayden's face with Anakin than it is to connect the previous actor.

Similarly, there is a plausible in-universe explanation too. Taking the 'Matrix' explanation of 'residual self-image' (in and of itself, a valid psychological concept), we can make a relatively short mental leap to applying that to Force Ghosts. Force Ghosts are manifestations of the person and their will. They aren't shaped by flesh and bone, but are creatures of pure mind. We see them as they saw themselves, at the end. Yoda and Obi-Wan, both very wise and possessing (presumably) good self-knowledge saw themselves as they were at the ends of their lives.

Anakin didn't have that. Anakin had, for all intents and purposes, been dead for a quarter-century. He was no longer Darth Vader, that mantle and the psychological pressures and deeds associated with it had been cast aside. What was left was Anakin Skywalker.

For Anakin, it would have been like someone in a midlife crisis, who still thinks they're the all-american quarterback they were in high school (and has that as their mental image) realizing that they're a slightly out-of-shape 40-year old car salesman. The years had changed his body, but not how he saw himself.

Since the Force Ghosts are creatures of the mind, he appeared the way he remembered himself being.

It is, at least, a possible in-universe explanation.