That's true about Pertwee's comedic background and I'd never knock his actual acting - if anything he brings a lot more warmth and humour to the part than the script sometimes would have it on paper. He certainly seemed to be a warm person in real life and was an actual spy, so I bet he really did love those espionage moments!
It's just those moments of Pertwee stories where he's boasting about knowing the nobility or like Day of the Daleks where he's poncing it up with some port and stilton that I really just get irritated with his character.
On the plus side I started watching Mind Of Evil tonight and that's turned out to be pretty amazing!