A lot of fuss was made about how Y'shtola was different now and how she had to have new clothes. I admit that could be for plot reasons which are nothing to do with jobs/classes/specialisations. Then a similar thing happened with Thancred where it's pointed out that he's lost the ability to cast his magic but his melee skills have gone nuts. Krile seems to be a 'Seer' which could be a new class or a specialisation of WHM. I'm really not sure on that one. Especially as Y'shtola seemed to be a conjurer before and Krile uses an orb
Personally, I think it's just that the Scions went from classes, to now having jobs, Thancred was a Rogue and may have had some spells, but now he is very Ninja-y, especially after training with Yugiri. It makes sense that the Scions are supposed to represent the trope of a well balanced party like other NPC parties from past FF games. The Scions at the end of 2.X were: PUG, CNJ, THM, ACN, ROG. Minfilia has not fought yet, so it's unknown what class she might be. The WoL, storyline-wise is probably a MRD/WAR since the archetype stand-in that represents our character in trailers is Derplander, who's a WAR. That being said, the Scions are starting to specialize from those PUG CNJ THM ACN ROG paradigms to be cooler/more focused. Since there's already 2 casters, no reason why the ROG should maintain their magic, and every balanced party needs a thiefy dextrous assassin character. The other Scions too are stronger and less generic after the events that happened post-disappearance. It's a classic anime trope. When a character disappears mysteriously for a long time, they reappear in a very' cliff-hanger', 'deus ex machina', 'save the day at the last second' sort of way, often times with new powers or abilities. This is probably a plot mechanic meant to make the Scions, of which the WoL is part of, a match for the Warriors of Darkness, which are all veteran adventurers. As we've gotten stronger in our 'absence' from 2.x to 3.0, so too must our allies. Just like Goku gets stronger in DBZ, they needed to upgrade Krillin and Piccolo too to make them not as lame, so they can handle fodder/cronies.