a system that gives you almost no say in what your characters do, encourages not making choices with the one character you do control
I don't understand what you mean by this sentence ? it seems to me you are describing the gambit system, comparing between FF12 and FF13 is meaningless because FF13 don't use MP points which encourage me to use different Classes,Paradigms and abilities while FF12 , it takes too long to unlock the most basic commands. It takes at least two hours just to unlock the ability to automatically attack enemies that attack you and there are some commands that you can miss entirely should you fail to find a hidden treasure chest or slay the right monster. FF12 only encourage players to grind from very beginning rather than progressing. Maybe i am wrong or over exaggerating .

One has a surprising amount of depth even when you let the game make most of the decisions for you, the other isn't much better than a game of rock paper scissors in that you have about three or four real choices of strategy in any battle and the best choice is always obvious and usually the same one you've made in every other battle.
No one is denying that FF12 offers more freedom and choices on micromanagement level but your average player spends his time to find right way to control partners commands, also you have unlimited time to slowly refine a macro system while the other one forces you have to make decisions during battles while time is running. I think FF13 sacrificed freedom and micromanagement for sake balance for all classes, IMO, FF13 is interesting because of the value of each classes combination, for example what is the value of com/com/rav vs a rav/rav/com ?

All you get is a strategically shallow battle system that does everything it can to have the player make as few decisions as possible.
All you get from FF12 a poor pacing battles without gambits, if you turn off the gambit system, the battles become REALLY boring. The gambit system is pretty much the only thing that makes FF12's battle system unique or interesting - everything else is just the most basic, vanilla turn-based combat imaginable. If FF13 is shallow then what is FF12 ?