I don't think it's any secret that all of us would want to have an entire universe under our control. So, we mortal men our stuck here writing about them. But are there downsides to having unlimited control in your fic? AU's provide interesting stories where the show couldn't go because of continuity. But are there certain lines one shouldn't cross when writing an AU fic?

3771363

The problem is thinking that it's unlimited control.

The first line that one can't cross is the one that removes the suspension of disbelief.

Can I believe that Celestia!Prime and Mirror!Sombra were romantically involved?
Can I believe that if Celestia went insane instead of Luna that 1,000 years later Trixie Lulamoon could be the Element of Magic?
What if Twilight went to Manehattan instead of Ponyville?
What if Octavia were the "number one student" of one of the princesses?
What if Twilight and another character (Spike? Trixie? Celestia? Rarity?) swapped roles?
Is it possible for a Pegasus (Scootaloo) to have a special talent in Magic?

Part of the storytelling is getting across that "in a world where..." the reader will still believe that the characters would act in a certain way.

The AU tag shouldn't be used as an excuse:

Twilight wouldn't act like that, sugar cube
Duh. That's why I'm using the AU tag, AJ.

If a known character is acting OOC, there needs to be a better supporting reason than "I wanted Twilight to be the bag guy in this story." Even in some of the good (YMMV) AU stories, the authors receive a lot of flak if Applejack becomes a tribalist magic hating plutocrat running Sweet Apple Corporation with Flim and Flam serving as batteries for the Super Easy Cider Squeezy 9001 (and occasionally sex slaves).

Note that perhaps one of the reasons the Good King Sombra comic worked (again, YMMV) is because the evil Mane Six didn't do anything important (and by doing nothing, didn't create unnecessary conflict).

3771363
Yes, there are definitely lines that one shouldn't cross. Some of those lines are just the standard things that you shouldn't do in any story, whether it's a fanfic or a completely original story. But those are just good writing habits that you should know about anyway (keep characters in character, avoid dues ex machina, make sure the plot makes sense...), so that's probably not what you're asking about.

I think you're probably asking about how this compares to writing a normal fic. For that, I say that you should start with what canon gives you and then take away whatever doesn't apply because of the changes you made to the universe.
For example, let's consider a hypothetical (well, as far as I know, this story doesn't exist) story where Celestia and Sombra have swapped roles. In this story, Sombra and Celestia will be very different from canon, so you'll have to write them differently. Twilight might turn out a bit differently because she has a different teacher, and Luna might be a bit different as well, depending on how her relationships with Sombra and Celestia are handled. And those differences will be what makes the story interesting and what the story should focus on. But everyone else will be basically identical to how they are in canon, and should be written accordingly. You shouldn't then use "it's an AU" to also make major changes to someone like Rainbow Dash, unless you can justify why the changes in your AU would make her act differently.
I think that it really comes down to really knowing the characters. If you really understand the characters, their personalities, and how their minds work, then you'll be able to figure out how they would behave under any circumstance.