There are two basic Doctor Who stories -- either 1) let's explore this strange place or 2) let's stop this alien invasion. #2 is the most common. But I was basically looking at an introductory piece. Because I was defying fanon, I would have to establish my own limits and so on since there was nothing else to fall back on. And an exploratory piece like An Unearthly Child was the best way to start. (By the way, I had to rewatch AUC for the address. I remembered the Totter's Lane part, but not the number.)
I also decided early on that any humor would come from the interactions. FiM is played for laughs. But almost any situation the Doctor finds himself in isn't played for laughs. The Doctor is a funny character in a serious situation. So I downplayed the cartoony nature in favor of the story.
Part of it was that I wanted Doctor Whooves to fit seamlessly into the FiM world. I just never cared for the idea that the Doctor was the actual Doctor who somehow regenerated into a pony. Yeah, cute idea, but not enough to hang an entire concept on. Plus, it just makes no fucking sense, and really opens some problems with the Doctor's archenemies stalking him.
Originally, I was just going to have him pop up in a situation Twilight and Derpy were dealing with, and they got to know him and became companions by the end of the story (yeah, I have more than one story in mind for this frivolity). But I also set a limit of 24 pages. Making the introduction natural instead of forced just took up way too much time in the planning stages. So I decided to cheat. Derpy's involvement was reduced, and Twilight became the viewpoint character. The backstory hinged on her history in Canterlot as Princess Celestia's favorite student. Given the amount of time and access she had with the Princess, she would see a lot more than others. The Doctor was someone who was an adviser and councilor to the Princess, but Twilight didn't know much more than that, other than he was smart, dedicated, and a decent guy. After all, the Princess hasn't revealed EVERYTHING to her faithful student. So when Derpy smacks into the building, Twilight calls on someone she knows to help sort through what happened. It also enabled me to show an air of familiarity and friendship between Twilight and the Doctor without having to show some sort of "get to know you" stage, it was already there.
That said, because Twilight became the viewpoint for my particular version of the Doctor, I still had to introduce concepts instead of them already being there. That meant doing a gag where she first sees the TARDIS is bigger on the inside than the outside. I think it's a law, every new character has to be shocked when they first step inside.
One thing I put notes in the script for was when Derpy had normal eyes instead of being walleyed. I decided that, when she was really focused on something, she would look normal, but her "default" mode was the derp expression. I also am aware she is depicted as not being the sharpest knife in the drawer, not just in the fandom, but on the show (her Nightmare Night costume and the bobbing for apples incident). I may not present her as Socrates, but I do show her being a little more on top of things than that.
Those of you who saw the original test drawings are probably wondering what happened to the TARDIS control room. After all, I had said I wanted to use the Peter Cushing TARDIS. I am technically still doing what I wanted to. There were two different TARDIS control rooms, one for each movie. The first one, to highlight the movie was in color (which was considered a big deal in those days) had all kinds of tubes and wires and other crap strewn around to make it seem science fictiony. I'm a minimalist. Trying to incorporate all that, especially in black and white, made it look like a mess. When I tried to focus on the actual props instead of just the Fienbergs, I noticed that the control room for the first movie was actually pretty sparse. It was only seen from one angle and the camera panning across it. You had a couple of computer-ish cabinets, and the scanner all pretty much on one side of the room. The only other things there were the control yoke, something that looks like an ATX computer tower, and the Doctor's rocking chair. I wanted a little more than that, and reluctantly started studying the control room for the second movie. It actually works much better. We never see the very back wall, but we see the other three (or enough of the other three) and get a much better idea of the layout. Also, there were fewer wires and extraneous bullshit (I did get rid of the piping, though). So still showing the lost Doctor some love.
The tendency in the fandom is to write Doctor Whooves as the Matt Smith Doctor (mostly because of the hair. It's not unusual to see drawings of Doctor Whooves wearing a fez). As I've said, I'm not overly enamored with him. There are others that depict him as the David Tennant Doctor. I liked him, but I couldn't quite get a grip on the character. My favorite Doctor is the Colin Baker Doctor (I still maintain that, if the writing had been what it was during Trial Of A Time Lord, he never would have gotten the thumb), but that didn't seem right. So my Doctor is ultimately just a creation that has what transcends every incarnation (brilliant spontaneous mind, a little bit of arrogance, sense of humor, etc.) without being a direct translation of anyone before him. I relied on that to get him across. I still think his line about, "Only someone lucid could see something so crazy," is such a perfect Doctor line.
Fast history lesson about the sonic screwdriver: the original (which actually appeared in a few Hartnell and Troughton episodes before being formally identified as a "sonic screwdriver" in The War Games) was simply a penlight from a local store. It was with the Pertwee Doctor that they started actually designing something. His and the Tom Baker Doctor's sonic screwdrivers were closer to ratchets, and with Eccelson, they went back to the linear design like the penlight. Since I'm working in minimalism, I didn't really need to use a design, especially if I wanted to use the first design. But it's a sonic screwdriver. If you tell people it's a sonic screwdriver, they want to see a sonic screwdriver, not some cylinder you can buy for $0.99 with a full tank of gas. Just like how no one wants a toy car of a Dodge Charger, they want a toy car of the General Lee. So I used Matt Smith's sonic screwdriver with the claw end instead of the rod shape of Tennant and Eccelston.
When I was collecting the Doctor Who comics from Marvel, I never liked how the depicted the TARDIS materializing and dematerializing. Especially the word they used for the TARDIS sound ("vwoorp"). Since I'm working in black and white, I don't have access to using layers and such to depict the TARDIS, so I fell back on showing it fading and seeing part of the scenery behind it as it went away, and no noise because I'm not sure how to describe it and anything I could use would be distracting as people reacted like me -- "That's not right!" Besides, he's technically a different Doctor, so I can just say he knows to take the parking brake off.
The one gag that always makes me laugh is when the Doctor is running through the list of things the TARDIS is impervious to. He originally just listed general phenomena like solar storms and such, but since they wind up underwater later on that page, I made a mention of floods. That seemed kind of mundane compared vortexes and plasma, and started running with it, coming up with other things the TARDIS was resistant to. For some reason, "kung fu" popped into my head as I was writing it. I stopped and just looked at the page, thinking, "The Doctor is actually explaining that a spaceship that can withstand the time vortex can also withstand kung fu," and started laughing. It is still my favorite gag. It's just a throwaway, but it's just so absurd.