Warrior and Soldier are already the same class. But, you might notice that no Bangaa class can be used by any non-Bangaa race, no matter how similar the classes are. So they will remain split.
Hmm... You're right, you didn't get a clear answer on the Chocobo mounts. The truth is that implementing them would likely involve changing the monster capturing back to the way it worked in FFT. That might work, but I'd have to get a few more opinions on whether or not to do that.
Anyway, here's the plot thus far: Our heroes start out in the Clan Center Headquarters in Cyril, discussing the attacks, and the collapse of the judge system. Ezel and Babus decide to work on a way to cancel the antilaws (despite Ezel's personal feelings against them [that part has been so much fun to script]). Shara and Ritz go back to clan Ritz, in order to ensure that there are as many forces as possible availible to defend Ivalice. The reason why so many defenders will be needed soon becomes clear: Defending the borders will not stop airships. The first battle is an attack against the Clan Center, and your clan for that battle is Marche, Montblanc, Ritz, Shara, Cid, Ezel, and Babus. You may notice that there are more than 6 people in this battle. You're right. Since the first battle here contains all of the secret characters from the last game (and Cid, Ezel, and Babus's abilities have been spruced up some [and they can jobchange now]), this battle is fairly easy. After this battle, those secret characters leave you, and you are left to organize the defense with the basic forces of Clan Ultima (or whatever you name your clan, as long as it is not Nutsy). The Area Freed missions from FFTA return, this time in the form of large scale engagements with Goltana forces (at least, for the normal areas. The cities have their own special sidequest...). The story quests start out as defensive engagements all over Ivalice, including an airship battle and a naval landing in Baguba Port. Your first Jagd fight comes in much earlier than it did in FFTA, and leads to speculation that the anti-laws that are causing all the problems may not be widespread enough for their entire army to use. Nevertheless, to win the war, Ivalice will have to go on the offensive...
I'm not going to show the script, because it is long, unnecessary, and I'm too lazy. If you guys want to put some scripting ideas up here, I'll pay attention to them, but I'm not going to stick my own script up here.
Going back to a technical aspect: I've switched the Judge Law abilities a bit. When fighting in lawful places in Ivalice, the Judge abilities will cost very little MP. However, when engaging far outside the normal range of Ivalice's laws, the MP cost will steeply rise, so you will have you use your judges well near the end of the game.