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Broken Base: Opinion is sharply divided amongst Doctor Who fans as to the quality of the film. From The Doctor being a human named Dr. Who, to the interior of the TARDIS, it's very hard to find common ground. However, most fans do agree that the production values, sets on Skaro and special effects are fantastic. And this one is usually regarded as better than the second.
Ensemble Darkhorse: Susan Who for being so much more badass than Susan Foreman.
Epileptic Trees: There are more theories on how to make Dr. Who canon than there are trees in the Petrified Jungle.
In the film, TARDIS' interior doors are those of the police box, as opposed to separate doors as they were in the classic series. Come 2005, and the TARDIS doors are those of its disguise.
The Dalek Supreme. The 2020 audio drama "Return to Skaro" would retroactively establish that there was a Dalek Supreme calling the shots in "The Daleks." It also had a black casing.
Narm Charm: Fans of these films usually fall back on this argument.
Taking full advantage of the colour technology provided by the cinema, the Daleks are all sorts of colours - which helped inspire Steven Moffat's Dalek overhaul. Likewise, Terry Nation had always intended for his creations to have Fantastic Caste System that was denoted by colour.
The Doctor as a human scientist. In the show's canon, the Time Lords had not yet been established and the only explicit detail about the Doctor's past was that he was not from Earth. It was a common belief at the time that he was from some hyper-advanced colony of Earth's in the distant future. All this film did was make explicit what most people believed (or a variation of what they believed) at the time.