FFT
Pros:
Stat Optimization: The appearance of level 1 recruits and the ability to lower character's levels to stat train differently meant you had far more character optimization abilities in FFT than you did in either of the other games.
Job System: The job system was well set up, and featured nice transitions from base jobs to more powerful ones. The unique jobs were plentiful and useful, and fitted well with their respective characters.

Cons:
Battle System: There was a fair amount of needless complication to the battle system, most notably the Zodiac system and the Faith/Brave system, and the Charge system really butchered the usefullness of a lot of jobs.
Ability System: Gaining abilities in FFT was one of the more annoying grinds I've done in a Final Fantasy game. While the job system itself was fairly well set up, the actual system for gaining JP was implemented poorly.


FFTA
Pros:
Balance: FFTA's job system was the most balanced of them all. Every job in the game was useful in some way, either for stat growth, ability set, or availible equipment. FFTA claims this over FFTA2's because of the change to the MP system.

Cons:
Item/Ability Acquisition: While I felt the method of gaining abilities was much improved from FFT, the fact that abilities were tied to items and items were acquired randomly meant that your clan could be crippled because of bad luck, or unable to find particular items for a very long time (I know that I didn't get Blizzaga until after I beat the game in my first playthrough).
Law System: While it was an interesting change to make to the battle system, the laws became far too restrictive, especially as you progressed to the game's end. Law Cards were hard to find, rarely matched up with the laws you faced, and too expensive to trade. That, combined with the severe penalties (in addition to losing units, you could lose items, exp, gil, stats...) for lawbreaking, made the law system too much of a hindrance to most gamers.


FFTA2:
Pros:
Law System: The law system was much more refined in FFTA2. The penalites for breaking it were much less severe than in FFTA, but the benefit to following them was still there. They would aid in combat while you followed them, but always in a small way, and the item rewards were small enough that players could ignore the law system without too much problem. They enhanced the combat system, they didn't dictate the way battles went (except in a few missions where you aren't allowed to break the law, but that was done on purpose).
Item/Ability Acquisition: I really feel that FFTA2 had the best ability system of any of the FFT games. The Bazaar system was much more thought out than FFXII's, and you could see exactly what you needed to unlock various items. Loot was easily availible (though never plentiful unless you used a lot of thieves), but not so abundantly so that you could unlock everything in a few missions. Rather than dumping all your loot on the first items you could unlocked, you were encouraged to look over what items you could get, and balance the need for those items over other items you could unlock. It gave incredible flexibility to the character customization system. When combined with the fixed rewards of the missions, it meant that finding particular items or abilities was far less of a hassle than it was in FFTA, and didn't need the long in-combat grind of FFT.

Cons:
Main Story: The main story builds slowly, introducing more elements, and providing an excellent learning curve for the game's systems. Then, around two thirds to three quarters of the way through, you get the feeling that the people writing it were told that they only had a few more missions left to finish the story. The climax builds extremely swiftly, and ends far too soon. There is a lot of plot info that I feel was left out, and a lot of potential for expansion of the main story that never occurs.