Given the nature of this subpage's entries, all spoilers regarding Turnabout Storm won't be marked, but spoilers specific to Ace Attorney and MLP: Friendship is Magic will.Fridge Brilliance
When Twilight chides Phoenix in annoyance for whining, he snaps, "I'm not whining, I'm complaining!". This is one of Rarity's lines in "A Dog and Pony Show". Guess who Phoenix bonds with most easily?
Rainbow Dash gets quite upset after Nick assumes she is an Earth Pony; the reason may seem pretty obvious, but there's another less obvious motive for her to be upset. The previous Rainbow Dash was an Earth Pony, and polar opposite in personality to this Rainbow Dash, who likely would be irritated with her namesake's behavior.
While it may be a bad thing that Celestia wasn't gonna be a judge for Rainbow Dash's trial, it turns out to be a good thing in the end, as Celestia probably wouldn't allow Phoenix to accuse Fluttershy in order to buy more time.
Trixie is pretty damn successful holding up her case in the first day of the trial; she manages to end with the upper hand the first day of the trial, something Ace Attorney prosecutors can't brag about. She could be considered a Villain Sue by some but then again, she does have an advantage over the prosecutors in the games. Consider this: In the games, all the prosecutors not called Winston Payne come with a pretty open and shut case at first glance, same as Trixie; and usually have a piece of evidence or testimony they pull off from nowhere after Nick finds a contradiction, destroying Wright's line of logic, same as Trixie; and Phoenix manages to break their case just in time by using either "unimportant" evidence he collected or a testimony from someone he spoke to while investigatingnote Or the occasional Big Damn Heroes moment, making him get the upper hand at the end. But it's different this time. Phoenix took this case on very short notice so he didn't get the time to collect said case-breaking evidence and he's very aware of it. Not only that but he's on an alien world and has little knowledge on its workings. Of course Trixie is being so successful; she has an advantage previous prosecutors never had over Nick.
Phoenix gets increasingly pissed at Trixie calling him Mr. Wrong; kind of strange, as he trends to shrug off insulting nicknames (like Godot calling him Trite). He's got good motives to be pissed by that nickname though, since he's been called like that before, by Mia Fey's killer no less.
Why is Phoenix so rattled when Pinkie Pie starts calling him Feenie? Because that's what his girlfriend used to call him. You know; the one who tried to kill him and then frame him for murder? It's understandable that he'd want to limit the number of people… err… ponies calling him that.
When Phoenix asked if Rainbow Dash had ANYTHING to do with the death of Ace Swift (note the use of "had anything to do") he's remembering back to Case 2-4: Farewell, my Turnabout, where his poor phrasing of his question let Engarde slip through the Magatama's effect of truth detection. He DIDN'T kill the victim, but had a hand in his death.
That Cupcakes reference, or actually how Phoenix saw it, seems completely out of place, considering that Maya is also prone to those sort of creepy commentaries without Phoenix starting to see red backgrounds with eerie zoom-ins. But after some thinking, it's sort of justified why he got nervous with it. Note how Pinkie has been calling Phoenix "Feenie" the entire time she's been with him, which happens to be the nickname his murderous ex-girlfriend used to call him. He's been having constant reminiscences of Dahlia thanks to this, and Pinkie's creepy comment made him make an immediate connection with her, thus getting him nervous to a extreme.
Pinkie stops Phoenix from saying Derpy's name during their encounter. Despite many fans believing this to be a nod to "Derpygate", after watching Part 3 - Twilight it becomes apparent that Pinkie simply knew the problems that would arise, since it's normally Pinkie's hobby to memorize a basic bio of each and every single citizen of Ponyville.
It's weird seeing Trixie's Black Psyche-Locks being viewed as a Tear Jerker when the previous (and around the time the episode was shown, only) person who had them was a Complete Monster. However, it makes perfect sense when you hear how Phoenix describes them when he faced the latter. One of the details he said to describe them was "full of despair". So in a sense, they're still the same, but in the former's case, that part of them is more remarkable than in the latter's.
It helps that the next character to have black Psyche-Locks in Ace Attorney's canon (Athena Cykes) is much more sympathetic than their original bearer Kristoph Gavin. Furthermore, the next bearer's locks are surprisingly similar to Trixie's.
Twilight admonishes Phoenix for cursing when Trixie revealed she knew the connection between Rainbow Dash and Ace, which makes sense when you realize that The Ace Attorney series is rated T, though the ESRB never mentions the mild language, while Friendship is Magic is marketed, usually, to little girls and thus uses unusual euphemisms for their swears.
This becomes doubly hilarious when Twilight again glares at him after one of the witnesses curses on the stand. Perhaps Phoenix's mere presence has upped the MLP universe's rating? note As if the murder hadn't already, of course...
Pinkie responding to one of Phoenix's inner monologues may seem like a silly off-hand gag, but she did have a good reason to know what he was thinking; after all, wasn't she the one that said later that she had read a good part of the script beforehand?
Phoenix teases Gilda during her cross examination since, as he said it, "Anger makes you stupid". This fits particularly well with the motives that lead her to tamper with the crime scene.
Rainbow Dash's anger at Fluttershy for testifying puzzled me. Then I remembered: "Oh, right. Element of Loyalty". Of course she'd take a perceived betrayal more personally.
From the element of Kindness, no less.
How come Trixie has formal education as a lawyer? Seems kind of off until you consider something Sonata mentions: That Unicorns from Canterlot generally take multiple jobs. Trixie's from Canterlot, so this would apply to her as well.
Then again, why study law? Isn't it an incredibly hard and time-consuming career? Remember something Twilight says in Part 3 - Twilight: Most crimes that take place in Equestria hardly warrant trials and lawyers. Unlike on Earth, being a lawyer in Equestria wouldn't exactly be a solid job choice to take. Chances are being an attorney is considered a secondary job for the ponyfolk at best, something easy they can study just because they can.
Sonata and Ace Swift are parallels to Mia Fey and Red White. Though Sonata lacks the moral character that Mia possesed, she still was almost killed trying to expose the asshole blackmailer. But in the far more idealistic world of Frienship is Magic, karma killed Ace for his crimes rather than Sonata.
In a similar light, the final confrontation turns from the final nail in the coffin for the antagonist it is in Ace Attorney's world, into a bringer of hope for the antagonist, and the thing that cements their Heel-Face Turn.
Regarding parallels, Sonata has another and very strong one with Lana Skye. Both stoic prosecutors that bear a strange resemblance to Mia Fey. Both not as cold as they let out. Both tampered with a crime scene in desperation and because of a misunderstanding of the events. The big difference between them is that, unlike Sonata, Lana did it in order to protect her little sister.
Sonata:Because the sad truth is... I don't have anyone to protect...
Something very curious about the events in the last scenes was noticed by a fan in the comments, which was then acknowledged by the author as a really neat coincidence:
Phoenix saying she was helping him find the truth = Honesty
Offering to see Trixie's magic show = Kindness
Trixie and Phoenix having a joke-off = Laughter
The fate of Phoenix's payment = Generosity
Twilight saying they'd be there for Trixie if she was ever in need = Loyalty
And what was produced after Nick went home = Well, you can probably put that together.
Twilight says that humans have such a commendable sense of justice that ponies based their justice system on the human's. Considering how much of a mess is the court system in Ace Attorney, and assuming that humans are not the only alien species that have wound up in Equestria, just how much must criminal justice suck for other alien species in this MLP and AA universe? And how harsh must have been justice in Equestria before contact with humans?
Banishment to celestial objects seems to be a popular form of punishment.
Speaking of… Would this mean that Luna killed someone before she was banished to the moon?
If we follow the argument that eternal night would lead to the death of all living creatures in Equestria, even if Nightmare Moon is not guilty of directly murdering anyone, she would be guilty of attempted genocide at the very least. It's also possible that some ponies already died as a consequence of her actions before Celestia could decisively defeat her.
I think it's more of like the Equestrian haven't needed a legal system to deal with crimes like murder and the court system in the Ace Attorney world, for all the wackiness one can see at times, works for the humans.
More a case of Fridge Sadness, but as funny as it is to watch Twilight flounder around during her conversation with Derpy, the idea that Derpy has a mental disorder that makes her believe that nopony bothers to remember her name is rather depressing.
Just the fact that Apple Bloom was around at the moment the events that lead to Ace's death took place. What if she had run into Ace Swift in the middle of his Villainous Breakdown?
What if Fluttershy had been a little late with saving Phoenix's butt in both occasions?
Interestingly, the bad ending contest had imagining this situation during her second Big Damn Heroes moment as its premise.
The story was written before season 2, and also takes place before it. Keep in mind that this trial is for the holder of one of six Elements of Harmony. If she gets banished to the sun, there might be no way to get her back to use the Elements of Harmony to take out a certain threat. Care to guess what happens when season 2 begins?
That's saying if she would ever want to help them after being betrayed by Equestria. Element of Loyalty, and general hothead who doesn't think before she acts and all. Also, Discord would probably taunt them about falsely imprisoning Rainbow Dash, maybe get the culprit to admit their crimes, and then laugh and laugh as the ponies lynch the pony responsible for eternal chaos.
The conclusion reveals that a defeat may have been a whole lot more tragic than first thought. Besides Rainbow being banished, we have:
Sonata. She would have walked away scot-free; but chances are that the guilt of making an innocent take the bullet for her, making a lot of other ponies suffer in the process, would have caught up to her sooner than later. She was already broken by the blackmailing and the fact that she thought she had killed Ace, so who knows what that would have done to her.
Trixie. If you interpret her as someone that deep down realized she was doing something wrong, but was too stubborn to admit it to even herself, she might have eventually been pursued by a strong and lingering guilt she would never admit to. If you interpret her as someone who needed to be set straight by Phoenix before starting to go through her Heel Realization, there's the chance that her victory would have been a strong Start of Darkness. Like Twilight said, another pony had been assaulted by feelings similar to hers before, and it did not end well.
Want some extra Fridge Horror? Looking at the state of her Black Psyche-Locks, the outcome of the trial could've very well decided who her AA-verse parallel (in terms of Black Lock bearer and psyche) would've been. Turnabout Storm's official canon has her paralleled with Athena Cykes, who, prior to having hers broken, had forgotten her secret but it still haunted her, traumatizing her. In the Bad Ending canon, she would be paralleled to Kristoph Gavin, who has his black locks whole and whose traumatizing secret had become so ingrained into his memory that it twisted him to the point of ending people's lives and careers for the pettiest of reasons.