The Doctor does mean they'd have a male intruding on the all female main cast (but he's too important to the fans to be ignored).
Let's say there are about 22 episodes in a season of the original show (ballpark figure):
Therefor, there would be 11 episodes in the spinoff series.
The episodes themselves would also be shorter: About half as long as episodes on the main show.
Finally (and here's a creative challenge for the MLP staff):
If they do it right, they could make it so that if you watched the second episode of the main show, which would correspond with the first episode of the spinoff series, you would actually see what the characters in each show were up to. They could even record dialogue for the background characters on MLP and the MLP characters in the background pony spinoff, and then turn it down to a barely audible level.
Oh and my thought about Derpy: She's actually secretly a very smart pony, who is badly treated because of her appearance. The mailmare job is just a ruse. She actually works for the Equestrian Security Agency (parody of the N.S.A) because being able to see double makes her quite good at solving complex math problems and speed reading. She's occasionally called on to prevent disasters before Celestia has to call in Twilight.
So Derpy has probably saved Equestria lots of times, and yet nopony even knows it.