Yeah, the regeneration isn't quite enough to judge an actor's portrayal. Also sometimes it takes a while for an actor to get the 'feel' of their Doctor. For instance in Spearhead From Space Pertwee was sort of imitating Troughton but eventually settled into the role by the end of the season. Peter Davison's portrayal of the Doctor in Four To Doomsday
and [I]The Visitation[/I-which were filmed earlier-is somewhat different from how his Doctor acts in the rest of the season.
Matt Smith also started filming the Weeping Angels story before his 'debut' in Eleventh Hour.
Even actors well established in the role of the Doctor can alter their performance based on the producer or head writer. Tom Baker is the best example of this IMO, he started off fairly serious but when he came under a new producer the stories got increasingly camp (with the exception of his final season, which was almost too serious).
Another example is Sylvestor McCoy. Although his first season is very campy, that's toned down in his second (Although it's still a bit silly) however his final three stories, Ghost Light, Curse Of Fenric and Survival-seem to be heading in a darker direction and Mccoy's Doctor seems somewhat more distant, somber and manipulative.