We all wanted Walt's creepy is-it-a-superpower control of the world around him to be fleshed out more. The birds slamming into the window of his stepfather's home in Australia, the polar bear that he just might have telepathically summoned, the Others' fascination with him (hello, Room 23) -- all of those things and more made Walt a pretty tantalizing segment of the mythology of Lost.
It'd be easy to say that he had to be written out of the show because he was hitting his growth spurt and the year-after-year filming schedule couldn't accommodate the changes to his appearance and voice considering a narrative schedule of a couple Island days per episode. But I don't think the showrunners, all strapping lads themselves, were so blind to human biology as to not see puberty coming. I take Damon Lindelof at his word: "We've always known Malcolm was going to grow faster than we could shoot the show. And we planned for it. Trust us."
So let's consider what actually made the cut before Walt left the regular cast. There's a specific question that we all found pretty fascinating back then that I think points to what was going on with Walt and the Others and all those tests. Beatrice Klugh, interrogating Michael, asks him about his son, "Did Walt ever appear in a place he wasn't supposed to be?" This just about sums it up if you ask me.
Walt and Michael are allowed to leave the Island at the end of Season 2, just as we find out that people are looking for the Island (most notably, Desmond's gal Penny). Throughout his lifetime, Walt is shown drawing things to him with the apparent power of his mind, or will. Things happen when he wants them to happen, if he really wants them to happen.
What would happen if he really wanted someone to find the Island?
Now you see why Ben and the Others were so terrified of him. First, they wanted everyone to stay on the Island so no one could disclose its location. But then they got wind of Walt. They wanted to test his abilities, discern the liability to their need to keep the Island's location a secret, and then pound it all out of him with Room 23-style brainwashing if necessary. When they found this wouldn't work, they cut him loose -- and in such a way that neither he nor his father could ever reveal anything about the Island.
And at the end of Season 3, when a freighter approached the Island and discovery of its location was imminent, who showed up on the Island, where he wasn't supposed to be?
L O S T
(Unless you think the manifestation of Walt standing over that DHARMA grave wasn't actually Walt, but I digress...)
I think it's a great way to write an arc for an actor you know can't last out the full sweep of that arc. In a show full of stories told but never really concluded, I don't know that the Walt story could have been handled any better.
Though, I should probably get around to finally watching "The New Man in Charge" before I say that. I'm just not sure I want the show to end.