Divine Beings
Nyarlathotep (Persona 2) vs Vergil (SaGa Frontier) - Vergil is immortal, but not necessarily -divine-. His powers are pretty nebulous and he likely has a lot of the same limitations that other Mystics do (apparently the inability to grow, at the least). Nyarlie is pretty powerful in a straight-up destruction fight, plus he has that pesky rumors-as-reality ability, and certainly becomes stronger as humans become more evil or suicidal or what-have-you, so the potential is better. Lovecraft 1, Mystics 0.
Lenneth Valkyrie (Valkyrie Profile Series) vs Cthulhu (Cthulhu Saves the World) - VP1 A Ending Lenneth is basically my baseline for "Most plot-powerful being in the DL". You have to spoil somehow to beat her, really. Lovecraft 1, Valkyries 1.
Superhumans
Tir McDohl (Suikoden) vs T260G (SaGa Frontier) - Speaking of Spoiling! Robots 1, Runes 0
Belial (Wild ARMs 4) vs Altima (Final Fantasy Tactics) - I think Altima might actually be a kind of divine being, and theoretically has access to more energy, but Belial, despite being mortal, has unique control over physics that can be applied in so many creative ways. And one of those ways just so happens to emulate the way Altima has been defeated before, so... Metal Demons 1, Bloody Angels 0
Warriors
Delita Hyral (Final Fantasy Tactics) vs Cliff Fittir (Star Ocean: Till the End of Time) - Cliff is just generally competent and supremely durable in battle. Klausians 1, Noseless Abominations 0.
Raquel Applegate (Wild ARMs 4) vs Aelia (Valkyrie Profile) - Agree with NEB logic here. Undead Warriors 1, Almost-Dead Warriors 0.
Civilians
Gina (SaGa Frontier) vs Anastasia Romanov (Shadow Hearts: Covenant) - And Gina's reign of terror through obscura finally comes to an end! Underage Princesses... uh... 1? ...and also 0?
Arnaud G. Vasquez (Wild ARMs 4) vs Tengaar (Suikoden Series) - Close match, but I'm giving this one to "Arnaud might hesitate to beat up a teenage girl". After all, she's not an -ADULT- (hiss! boo!). But there's no way Tengaar would hesitate to bitch-slap a dude. Drifters 0, Runes 1 !