Even by the end of Tom Baker's first episode, I preferred him to Pertwee. I loved the 3rd Doctor's character on paper, but Pertwee had limited range and didn't do much for me. I didn't dislike him by any means, but I liked Hartnell and Troughton so much more. It also didn't help that most of the 3rd Doctor's stories were really weak and formulaic, with the exception of his final season, which I felt was a noticeable improvement. Since I'm watching this stuff for the first time, I have no opinion of the later Doctors in the classic series yet.
I'm towards the end of Genesis of the Daleks right now, and I've liked every story so far this season. It took me forever to get through the 3rd Doctor's era, but I'm getting through the 4th much faster, because his energy and charisma make it a lot more enjoyable.