Phoenix has to decide whether or not to administer Justice to Matt Engarde, or to do his job and plead Not Guilty - a decision ultimately left to the player.

Godot.

3-1 Feenie coming to the realization that Dahlia is psycho/didn't love him/tried to kill him
3-4 Mia losing her first case/Diego going into a coma, Dahlia escaping, Terry dying
3-5 Of course Godot's arc, Dahlia realizing she's a loser, Maya losing Misty

In T&T, certain characters are trying to discover the truth to some incident in their lives that deeply affected them.
3-4: Shows the beginning of Mia's struggle as a defense attorney, as well as Edgeworth's beginnings. I think this trial kind of showed us the harsh world the two lawyers were introduced to since day 1. Ever since then, Mia had been working with Godot to find evidence against Dahlia, and Godot's poisoning followed soon after. Mia was so traumatized by the trial and Godot's fate that she didn't step foot into the court for a year.

3-1: Mia was trying to bring Dahlia to justice for poisoning Godot. As a result though, Dahlia plotted revenge on her. At the same time, Phoenix thought he had been deceived by Dahlia all this time and was dragged into an unnecessary mess, probably wondering why things turned out the way they did.

3-5: Phoenix sees Iris' picture and realizes he has a lot of unanswered questions about the hurt and betrayal from 5 years ago. This case was spent digging up the past. By the end of this case, Phoenix received his answer, and his past has been dealt with, and he could now move on from the memories. At the same time, Godot could finally live with himself as his resentment toward Phoenix has finally subsided. He made peace with Phoenix and Mia and his sorrow is over.

This game in particular reveals a lot about characters' struggles and ghosts from their pasts. (e.g. Mia, Godot, Dahlia/Iris, Phoenix, Misty, Morgan, etc.) In the end though, they each struggled through the hardships to finally reach the truth. I guess that's what this ending is all about essentially. Truth has been brought to light after you witness everything the cast went through since GS1.