FFTA
Pro: Job UI. I have no idea why the changed the job UI when going from FFTA to FFTA2. It was the same mistake I feel they made when going from FFVII to FFVIII. They go from a nice, easy to pick up, visually appealing system to a purely text based one (Materia to Junction systems for those games). The progress bar is ok, but I really liked the ring selection of the jobs and the stars indicating job mastery. A colorful interface is usually preferable to a bland text one.

FFTA2
Con: FFTA2 loses additional points on the UI for having a broken job mastery indicator. The job mastery progress bar only took into account A-Abilities, which means that you could "Master" a job without knowing any of that job's R-Abilities or S-Abilities, which was a big no-no. Without a strategy guide, it would be nearly impossible to tell whether or not you had every R or S-Ability a job had to offer until you had collected all of the gear in the game, which is a very daunting task.

Pro: This may apply to FFT as well, don't remember, but giving unique classes additional abilities to learn was great. It kept the unique jobs versatile and powerful enough to keep up with the rest of the jobs in the game, without overpowering the unique characters when you get them (as would happen if you had all those abilities in the beginning).