Ultima is at a lower level than Zodiark, but she's way more adaptable. Whether she's tougher or not depends mostly on how you play. Be prepared for absolutely anything and bring lots of remedies and x-potions (she can and will nullify your magic). Gambits are a mess during Ultima if your'e not familiar with how she behaves. The most important thing is to have white masks or sage's rings on everyone so they absorb Holyja. But, yet again, Holyja can still cause reverse even if you absorb it. Make your top gambit ally status = reverse > attack.
Personally, while I really like Ultima as an esper, Ultima and Omega Mk. XII are always the very last thing I do before clearing the game. Namely because I !@#$ing HATE the Great Crystal. The monsters there aren't as bad as those in the Henne Mines though. Those are sick.
Another thing to add, you should try to pick a magic field (I recommend the technique one) to go 'all-out' on her while you use the other 3 fields to heal and survive. I found Ultima much harder than Zodiark but that was because I get impatient with boss battles. It's a longer battle so be ready. Umm, the Mega-Potions/Mega-Elixirs can come in handy for emergencies so if you've saved them up, give yourself a pat on the back. Just don't use any ethers or elixirs when she has the Drain MP or No Magick fields up.
And when she brings up the Drain MP field, immeadietly start a quickening chain and heal with items. I also suggest getting magick that deals non-elemental damage or/and Darkga as she's pretty strong against elemental damage (save for dark, she's weak against that). Here, I'll give you a handy-dandy walkthrough link (if you want to use a walk-through):
http://www.gamefaqs.com/console/ps2/file/459841/46240
After going to this link hit "Ctrl+F" (by the way, incase you didn't know, you CAN use this key combination to search up anything in any walk-through. This key-combination has saved me LOADS of time) and type in "Ultima". This link will give you a great strategy for her as well as give you an idea as to how you should set up your gambits. Enjoy.
Like Fatalis mentioned, The Great Crystal is a big pain in the ass. The only thing I enjoyed it for, was the well-suited music. I did something very stupid once and got 2 Moon Rings there. It took a good hour and half of my sanity. Never again, will I think of that horrible place. So when you grab Ultima, it's a great idea to get Omega as well. Unless you like the Great Crystal....