DM: As an alicorn, you'll have a mix of earth pony, pegasus, and unicorn traits. And yes, that includes the ability to fly up to your movement distance. Though you might have a debuff for being so new to flying until you get used to it.
Twilight Sparkle: That's fine. I don't think my ability to fly is going to make or break any boss fights. I'm okay being an alicorn-in-training.
Applejack: So, Ah take it y' don't want us to call you "Princess" or "Yer Highness" or anything.
Twilight Sparkle: Yeahhh, no. I mean... If other ponies want to call me Princess Twilight or whatever, fine. I've gotta get used to that. But not any of you. I mean, this happened because of your help, and our friendship. You're all peers to me.
Pinkie Pie: So... Honorary Princesses? Woohoo! I'll be the Honorary Princess of Parties!
Rainbow Dash: Sure, sure. Could you stop being so dang noble, at least? If you don't act at least a /little/ corrupt, I'm worried it's gonna rub off on me.
Pinkie Pie: My first decree: AT LEAST ONE PERSON HAS TO HELP ME CLEAN UP AFTER!
DM: Can I also make that demand?
What do you think would be a good temporary debuff for Twilight's initial flight ability? I ended up brainstorming a few mutually exclusive ideas in the process of this.
1. Her maximum height above the ground is limited to her move speed. Any higher and she falls back down to her limit at the end of her turn, making a roll to catch herself in mid-air.
2. When flying, she can't take actions more complex than At-Wills without losing her concentration. If she takes an Encounter or Daily action, she needs to make a roll to avoid falling.
3. Landing safely is never a guarantee. She can stay in flight as long as she is physically able, but when it comes time to land, she needs to make a roll or face (minimal) falling damage.
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I'd say just crib the rules for running (each move action to fly lets you move your speed and you take a (what was it?) -5 to AC, do it twice in a turn and it's -10). And then, because it's such a large penalty, have the thing taper off (one milestone later, it's -4 per fly action, two milestones, it's only -3, etc.).
Of the three options you listed, though, I'd go with 2 (follow-up question: if she launches a Daily with a Sustain Minor on the ground, can she later sustain it while flying?).
I admit I'm not well-versed on the rules, but in terms of cutting down Twilight Derails, 2 seems the best option. 1 and 3 give her indefinite air capabilities, even if 1 means she can't always be out of reach. 2 also feels like it makes the most sense under the 'pat your head and rub your tummy' principle, and the roll means she has to actually make tactical choices on if it's worth it to fly.
I feel like the closest match for what we see in the show would be to force her to make skill checks (which she isn't allowed to take ten on) to fly at all. The details on how to structure it would need some consideration, but that general idea is how you get the property that she could lose control and fall out of the sky completely at random because she's just not very good at this.
Ya know, I always thought Flight was an at will ability in Equestria, as evidence by every stressful flight situation:
Rainbow can't do the Sonic rainboom, despite being the spource of the thing in the first place. Her mental fear kept her from doing it, that doubt. But then seein Rarity fall, Rainbows only thought was "I NEED to catch her" and she flew the fastest she's ever flown. Rainbooms got clocked in by math-ier bronies after, all of them are slower than the young flyer comp Rainboom. Rainbows will made it work, and keeps making it work.
While more stressful for Pinkie, the infant who flies better than most adult pegusi is absolutely evidence. All the kid wanted was "up," and then it was the game of "keep away." Without the mental barriers of "I shouldn't be here, I shouldn't be flying like this" the infant was uninhibited.
My last evidence for this theory today: Tirek Vs Twilight. Twilight shows in the start of the episode that she still can't fly that well, and her magic is all kindsa wonk after the plan to make her the vessel. Then Tirik attacks, and Twilgiht flees. Her flight is poor in these moments, but enough to keep her alive
Then we lose the library.
Fight part two, and Twlight is doing advanced flight: Quick turns, sharp dives, and combining it with teleport to move with momentum! In her mind at this time, her thoughts weren't about how bad of a flier she is, weren't about how she wasn't ready for this.
This devil needed Smiting, and she had at!
I know it was probably an animation error, but if you want even more evidence, consider that Rainbow didn't use her wings for her record-setting rainboom. She was concentrating so hard on catching Rarity that she just channeled her pegasus magic directly and stopped using her wings as a crutch.
I feel like that was kind of the point. Physiology and physics have zilch to do with it, because wings and flight speed aren't a factor. As fits with the example given: "Rainbow didn't use her wings for her record-setting rainboom." lit., wings don't have anything to do with it.
So, instead, it'd all be magical strength and personal talent. Rainbow can go rainboom because her magic and talent are specifically set up to let her, not because she's physically a better or faster flier.
What I've seen pointed out is that when Rainbow failed the Rainboom in the episode, she always had one hoof forward, and the other three back. When she succeeded, she had both forehooves forward. So it could be a matter of hitting the air with just the right shape...
There are some creatures with a fly speed in 5e that have a penalty where they can't hover so they have to take off and land as part of their movement or fall out of the air. Maybe something like that?
I quite like the idea of failed flight checks leading not to damage, but to falling prone (which seems to fit better with the cartoon's setting).
A flight ceiling doesn't make a lot of sense for Twilight, who apparently has Teleport as an At Will, meaning that being high enough the ground to have time to react gives her more opportunity to recover.
Both 2 and 3 (with falling prone rather than taking damage) seem plausible and fitting - particularly with Twilight's tendency to overthink things and get in her own way as a result.
I did once see an interesting houserule to limit inherent flying characters. It was a feature called "Labored Flight" which made it so that you could gain your flying speed as an action, strung together to prevent falling. It could eventually become circumnavigated with a special racial class (it was a Legend of Zelda rule set for playing as a Rito). More or less a way of implementing option 2.
Maybe just limit her to half the max flight speed without a roll and have an athletics roll to take off, land, go faster than half speed, or do anything strenuous with flying.
1. Her maximum height above the ground is limited to her move speed. Any higher and she falls back down to her limit at the end of her turn, making a roll to catch herself in mid-air.
2. When flying, she can't take actions more complex than At-Wills without losing her concentration. If she takes an Encounter or Daily action, she needs to make a roll to avoid falling.
3. Landing safely is never a guarantee. She can stay in flight as long as she is physically able, but when it comes time to land, she needs to make a roll or face (minimal) falling damage.