I hope we're not derailing the thread too much with our side discussion about old Who.
Ah, but that's the point, isn't it? A bit of slapstick clowning is very obvious but it's a cover for a more complex and serious character.
I'd say it's more a part of a complex character. And I suppose it's always been part of
Doctor Who, which even in the old days could be very dark and disturbing at times.
It's one aspect of the show that immediately appealed to me when I started watching the new series - a really tragic story (the Doctor has lost his homeworld, is traumatised by the most horrible war imagineable and he keeps losing those he holds dear) is told in a light-hearted fashion.
Peter Bryant is on record as saying that he cast Pertwee deliberately on account of his comedy background because he thought it would lighten the show up, as it had been getting too dark at the end of Troughton's time.
Someone should have told Barry Letts and the writers.
I've only just finished watching Pertwee's second season but the stories aren't exactly light-hearted. The huge death toll among UNIT members and also civilians, the Master trying to destroy Earth in every story of the second season, the Brig mass-murdering the Silurians, the Doctor finding himself in mortal danger every other week (the cliffhangers are really kick-ass), evil corporations and oppressive governments - not very light material. Now, I agree that the tone in which those stories are told is light-hearted - thankfully, because otherwise it would be nuBSG. There's always room for witty remarks, like the great banter between the Doctor and the Master, and for elements not to be taken too seriously (Bessy, the Master listening to rock music on his listening-in device etc.).
However, I think that the Third Doctor is a much darker character than the Second. He's mostly interested in getting his Tardis working again and ready to betray the Brig in a heartbeat (in the first story already where he would have left Earth in a critical situation after lying to Liz Shaw to get the Tardis key). His frustration and bitterness about being stuck on Earth is quite evident. I'm thinking of the Doctor's last line in
The Mind of Evil, where he summarises that the Master can move about freely again while he's stil stuck on Earth. Pertwee plays the last part of the sentence light-heartedly enough so that it's not a total downer, but still. In
The Claws of Axos when it appears as if the Doctor had betrayed humanity to save his own skin, I felt it was very believable that he could do it.
I left out some of the stories where hardly any video material survives but I fail to see how the stories of the Second Doctor became considerably darker towards the end. To me, it felt like the usual mix of darker and lighter stories, just like during the Hartnell era.
Anyway, I never said Troughton wasn't comical - all the Doctors have been - but that Hartnell played it much more in that direction.
Well, art is perceived in different ways by different people, and that's great. I don't agree but I would be quite interested in hearing some examples if you have any in mind.
) and that's why it worked emotionally. I certainly didn't shed a few tears when Ten died because the Doctor now had one less regeneration but because I had connected with the character. 
