Patrick Troughton's final season begins on the 10th August 1968 (9 weeks after the end of Season 4 on the 1st June), and is 44 weeks long.
One thing to notice about Doctor Who's viewing figures is that although they still span almost a whole year, they don't appear to be affected by seasonality. At this stage in its existance Doctor Who is being shown at 5:15 on a Saturday night, which means in the winter it's dark, and in the summer it's light. Fan discussions in the 21st Century often focus on whether the show will get better ratings if it is shown in the winter, but as we can see from the last 6 seasons, this doesn't seem to have much bearing. The first story of Season 6 ("The Dominators") begins and ends with 6 million viewers, while the last story ("The War Games") begins and ends around the 5 million mark, with a dip in the middle to 3.5. Both of these stories debuted roughly in the spring/summer, although "The War Games" did run from April to June.
There is however a season peak of 9 million round about the end of December, with "The Krotons", a somewhat fan-disregarded story. However if we were to argue that this was down to the mid-winter favourability of Doctor Who we would expect to see a similar peak at the same time in Season 5, and we don't.
As an aside, there does appear to be a clear dichotomy between fan-regard of Troughton episodes, and the viewing figures of the time. Fan perception may well be due to the fact that a lot of episodes from the period 1966-1968 are missing, and a lot of those tend to be highly regarded by fandom, possibly because they only exist in the memories of those who have seen them. The reality though is somewhat different. This is black & white 1960s television we're talking about after all. "The Krotons" and "The Dominators" are derided by fandom, and yet the figures show them to be acceptable viewing at the time. "The War Games" on the other hand, highly regarded by the fans, is the worst performing story of the season. Once more the Cybermen story performs no better than the one before it, and worse than the one after, again belying their status as iconic classic monsters.
Although like its predecessor, Season 6 hovers around the 6 million mark for most of its run, it has to be said that it does have more troughs than peaks, and the overall viewing trend is down.