At the start they were trying to write him as 'her was basically good and flawed but he was becoming truly evil over time', it was supposed to be a character arc. This was the idea through season one and two, and there is still some evidence of it through season three and four.
Later they decided to go with 'he was bad all along but he only got a chance to show it later in life', not really much of a character arc, and kind basic as a character study. This was the main focus after season three, it's just that there was Gus to compare him to so he still came across as sympathetic up until Gus was killed.
Who knows why they changed it?