I would have to agree that FF III would definitely be the toughest of the main games.
Followed immediately by FF I depending on which classes you choose at the start (three Fighters and a Red Mage does not make for a challenging game but a full Black Belt party could easily surpass any other challenge in any other FF game).
FF VIII would probably be next until you figured out that the game can only be played by abusing Limit Breaks.
FF T would best fit here as it remains challenging until you get Orlandu and even then it gives it self a renewal of challenge with the deep dungeon, and it provides consistent challenge throughout the game without having to rely on game breaking factors (like rendering everything but Limit Breaks useless)
FF II & FF V are about equal in challenge as both require massive amounts of grinding to be in good standing for the final areas. But FF II loses points due to those Blood Swords, and V gains points for its hidden bosses Omega Weapon and Shinryu.
FF XII belongs here mostly for all the extra stuff (also since you can walk right out of a major battle with one of the hidden bosses to regroup) along with the fact that you really can’t do much with the License Grid.
FF IV is the next one with mostly due to the lack of the ability to create gods out of your characters along with extra fiends to battle after surpassing Zeromus.
FF’s VII and IX are about equal in challenge, FF VII has the Weapons and IX has Ozma and the constant railroading.
FF VI and X are near the bottom mostly due to the fact that it’s very easy to overgrind your characters into gods.
FF X-2 is even lower then VI and X by virtue of having only three playable characters to manage instead of seven or fourteen.
FF CC and TA do have some challenging moments, unfortunately for MQ the hardest part was finding all the necessary parts needed to play the damn thing and for TA it was enduring the boring mindless repetition.
FF MQ inhabits the lowest rung for being such a beginners game despite having more overall challenge than TA.
I haven’t played XI or DoC yet, so I can’t give appropriate evaluations to their difficulty level.