No, I don't believe Ultimacia to be the toughest, I'll give it props for being one of the most interesting boss fights in the series. Well I would say Yu-Yevon is hands down the biggest joke of a final boss battle in the series (And I'm counting the battles with Final Aeon Jecht and the Corrupted Aeons as part of this final boss battle).

The hardest battle has to be Zeromus from FFIV (Hard Version) just because the survival rate of your party is based on Edge stealing that damn Dark Matter off of him. Possessing the Dark Matter makes Zeromus' Ultimate attack "Big Bang" fluctuate in damage. If you don't have it, get ready to watch as Big Bang K.O.'s an average of three party members every other round.

What makes this really difficult is that Edge has absolutley no defense. Neither Physical or Magical so almost every one of Zeromus' attacks will kill him if they hit. The second problem is that Edge is a ninja first (and a poor one at that) and a thief second (He's definetly a better ninja than a thief and that means trouble for you) So it may take several rounds for Edge to successfully steal the item.

The next most challenging is probably the Cloud of Darkness from FFIII. If you don't have the right party set up, she will completely own you in one round. It's one of the few boss battles (As well as Zeromus) where if you don't come in with a strategy, the boss will pick you apart.

Every other boss fight in the series can either be won by discovering a trick or abusing the game's system. I mean Sephiroth can be beaten with a spam of level 4 limit breaks or just using Knights of the Round, Kefka can be beaten by spamming Ultima, Ultimacia is all about spamming with Limit breaks combined with good Junctions to stay alive.

The Emperor in FFII is a joke when you realize that the Blood Swords do insane amounts of damage to him. Chaos is flimsy so it more about buffing your Knights and staying alive. Neo X-Death can be defeated easily with eiither a spamming of Gil Toss or using the insanely overpowered Flare Sword/ Two Sword/ Barrage combo. Necron may hit hard but his attacks have the unfortunate side effect of raising your parties Trance Gauge twice as fast and as many know, if Steiner, Zidane, or Vivi goes into Trance, most battles is quickly over and it's really funny when all three go into Trance.

The Undying is not much of a fight but more of an endurance match (which is what most boss battles become 3/4 of the way through XII) and if you were smart enough to actually complete most of the Mark hunts, your party is probably better equipped and leveled than this fight actually calls for. Most boss battles in this series are pretty easy, it's just about finding the right strategy or trick. Or in most cases, abusing the game's broken battle systems