Er. Well, Patrick Troughton was the Doctor...
It's a bit odd; The Power of the Daleks did its best to establish that this strange man was in fact still the Doctor, but now The Highlanders seems to delight in taking the character and pushing it as far as they can. So Troughton here portrays a character who seems to be interested in causing trouble just for the hell of it. He tries to get the Highlanders on his side before denouncing them loudly (yes, it's a ruse to get out of the prison, but still), he goes around slamming clerks' heads on the desk under the pretense of medicine, and he dresses up as a woman to move about unnoticed. That's after he pretends to be a German doctor named "von Wer" (and anyone who knows German will see that Gerry Davis has struck again) but with only a passing attempt at any sort of Teutonic accent. It's a wonder Ben still has any faith in him.
Meanwhile, Polly becomes decidedly mean-spirited, repeatedly berating the girl Kirsty for crying and calling her a "stupid peasant" after she refuses to go along with Polly's half-cooked scheme about getting money to bribe guards. It's not very pleasant. And yes, maybe Kirsty is a bit weepy, but given that this story takes place during the immediate aftermath of Culloden, I think it's safe to say she's had a harder day than Polly has.
And I should probably mention Jamie McCrimmon, seeing how important he'll become to Doctor Who, but to be honest here he's just one of a cast of guest characters designed to take up (story) space while the Doctor and Polly get on with the real story -- Ben's stuck with them, but he's mainly an eyewitness rather than a proactive player in these first two episodes.
But it's not just odd characterization; you get the sense that the production team don't actually believe in the idea of an historical story. Traveling back in time isn't about learning things any more; it's about a place where you can have an adventure romp, because watching Troughton clown around for a while is apparently intrinsically more entertaining than actually exploring history. The days of The Massacre are long gone.
You can sum up this attitude with the fact that it's not The Smugglers, a story about 17th-century pirates, that has a pirate captain walking around actually saying "Arrrrrrr": it's The Highlanders.