Dawson Casting: Daniel Anthony at 20 and Anjli Mohindra at 18 play 14-year-old (at the start of the series) Clyde and Rani. Averted with Tommy Knight and Yasmin Paige being close to the age they play (though Luke was "born" in the first episode).
"The Wedding of Sarah Jane Smith" was supposed to guest-star Nicholas Courtney as the Brigadier, thus giving us a potential meeting between the Tenth Doctor and him. Alas, Courtney suffered a stroke before the shooting, and his part was scrapped.
Conversely, the episode that did feature the Brigadier, "Enemy of the Bane" was originally written for Freema Agyeman's character Martha Jones, and was rewritten for the Brigadier when Agyeman became unavailable.
The CBBC originally approached Russell T Davies asking for a Doctor Who spinoff involving a young Doctor on Gallifrey. Davies rejected the idea, feeling it would take away from the "mystery" of the Doctor, and proposed The Sarah Jane Adventures after a positive experience working with Elisabeth Sladen in "School Reunion".
As revealed in a Doctor Who Magazine special issue focusing on the show's cancellation, if the second half of Series 5 had been completed, the first story entitled "Meet Mr Smith" would have seen Mr. Smith become human and the season finale "The Battle of Bannerman Road" would have revealed Sky as being the child of the Trickster, who had interfered with the Fleshkind's creation of her; he would be finally vanquished after possessing Sky while Sky ascends to a higher level of existence. (Dialogue hinting at this was recorded for The Man Who Never Was but cut from the broadcast episode.) Oh - and Rani and Clyde would have got together. (RTD was less keen on completely detailing what the second story, "The Thirteenth Floor", would have entailed in the special issue because he decided to transplant the story over to Series 2 of the show's non-Doctor WhoSpiritual SuccessorWizards Vs Aliens.)
According to Doctor Who Magazine, other episodes planned prior to Sladen's death included a return appearance by Sophie Aldred as Ace, a live Halloween episode, and an episode featuring Tom Baker, though not necessarily as the Doctor.
The villain in "Secrets of the Stars" would originally have been a tool of the Mandragora Helix from the Doctor Who story "The Masque of Mandragora", in which Sarah Jane was the companion. It was then decided that it would have been too old and obscure a continuity reference.
In 2014, Tom Baker revealed that he had been asked to reprise his role as the Fourth Doctor for a episode of SJA, and had more or less agreed to do it, when Lis Sladen passed away.
According to Doctor Who Magazine, Matt Smith was to have appeared as the Doctor in the first episode of Series 5, "Sky". Due to his commitments filming the parent series, he was unavailable so the previously established character of The Shopkeeper replaced him.
Word Of God (primarily series creator Russell T Davies and scriptwriter Neil Gaiman) is that the character of The Shopkeeper is the Corsair, a gender-changing Time Lord first referenced on screen in Gaiman's Doctor Who episode "The Doctor's Wife." This was a retroactive decision, given the Shopkeeper's introduction predated Gaiman's episode, however Davies had intended for the Shopkeeper to make further appearances on SJA.