While the Sixth Doctor's use of violence and his abrasive relationship with Peri were both often criticised by fans, the violence was largely in self-defence, and his relationship with Peri had mellowed by the end of his time on the programme.

The Sixth Doctor's era is noted for the decision of BBC controller Michael Grade to put the series on an 18-month hiatus (effectively cancelling it) in order to fund a new soap opera about cockneys (and because he beleived all sci-fi to be total rubbish). After an outcry by the public (including a terrible disco appeal sung by members of the cast and crew) to return the show to broadcast, Grade relented and the 6th Doctor returned in the 14 episode epic The Trial of a Time Lord. This was to be the final series for the Sixth Doctor, however, as Grade fired Colin Baker in revenge for his active part in gettign the show back on the air.

Because of his brightly coloured, mismatched clothes and a brash personality that set him apart from all his previous incarnations, not to mention the events surrounding the near cancellation of Doctor Who in the mid-1980s, Colin Baker bore the brunt of the blame as the "unlikeable" Doctor for quite some time. However, the Sixth Doctor's return in the Big Finish Productions audio plays, voiced by Baker, have gone some way to changing this impression, with the Sixth Doctor appearing to be a somewhat calmer, wittier and altogether happier character. In a 2001 poll in Doctor Who Magazine, Baker was voted the "greatest Doctor" of the audio plays.