That's a good point - Anakin's transition to the Dark Side made no sense. He was reluctant to switch over, then basically the first thing he did was slaughter the Jedi children!?!? That's not a transition...I think the thing I liked about Eckhearts performance the most was how he was able to present this "whiter than white" image but there was always that sense of darkness inside him. Even before his scarring there are scenes that imply his ruthlessness, for example the coin toss in the alley way scene and how he already had a reputation for being Two Faced. He was such a well fleshed out character that his descent into darkness didn't seem artificial unlike some other efforts... I'm looking at you Anakin Skywalker.
But like you said, everything about Eckhart's performance made sense.