Yeah, I'd say Lenus is the toughest mandatory boss for me. She's really fast, and she can use water magic on Dart. It also doesn't help that Meru doesn't have her dragoon form yet. Strangely enough, she gets weaker with a dragoon spirit and the help of a huge sea dragon. Go figure.
Overall... I'd still say Lenus. The Divine Dragon Spirit can be tough, but you have some more options at that point, at least. You can have your additions mastered, and Meru has her dragoon form to heal easily, unlike the Lenus fight.
Maybe you gave Lenus more of a walloping than she let on, so she was still hurt when she went Dragoon.
Lenus and Divine Dragon Spirit are kind of opposites. With Lenus she'll go berserk if you dragoon, and DDS will just eat you if you don't dragoon. It's pretty much entirely because he can bust out the cannon whenever he wants to.
Jiango, Doel and Lenus. These three always give me trouble whenever I do a challenge run. Especially Jiango. That guy somehow gets to double me and use that stalagmites thing twice and poof, my party's dead.
Doel's Spark Net is ridiculous. I saw it OHKO Rose at full health on one of my playthroughs.
Lenus can be a bit hard but it's manageable. I manage to beat her solo using Meru with Therapy Ring. The battle was too long since Meru only had a Lv. 3 Double Smack but Lenus can't kill Meru.
"I believe that stories are written and read to rebel against the fact that you only live once."
Well, first time playing Drake the Bandit killed me twice (I was 10.) After that, Django (Jiango) owned me. Then Lenus killed me. In subsequent playthroughs I killed drake and magicked Django to death but Lenus still took me apart. My boyfriend once attempted lenus and she decided to have 7 consecutive rounds. Needless to say he died. She's definitely the hardest mandatory boss.
As far as optional bosses go, I found Kanzas to be the hardest. Fast, strong with both magic and physical attacks, and no weaknesses. He ruined my day unless I kept the most balanced party in the game, or had Albert and Meru to protect/heal.
I never found Faust too difficult. He's more in the category of "tedious boss fights that go down quickly (relatively) but can end at a moments notice," kinda like Ozma or the "Meat Jesus" fight in Shadow Hearts.
Into the ray of the sun march our hero hunting the dark lord, reborn from the blood of his god, his god, the war-master Kron...