Godlike
Profound Darkness (Phantasy Star IV: End of the Millenium) vs Shania (Shadow Hearts: From the New World): Everything about the final form is something Shania hates (holy damage, dispel, a status she can't block). No one of those spells instant doom to her game but I really can't envision her getting through this, similar to PD vs. Yuri.
Sephiroth (Final Fantasy VII) vs Terra Branford (Final Fantasy VI): Paralysis on the ITE fast physical.
Indalecio (Star Ocean: The Second Story) vs Cloud of Darkness (Final Fantasy III): While it's true that Indalecio can clear out one of the tentacles pretty well (the second is immune to magic, so no dice there), this still feels like a bad matchup for him? CoD has great damage control and can also buff herself with Haste against form 1 after which she can do 1.4 PCHP a round. Indalecio isn't getting off more than one Explode and two basic spells and that's not even close to enough to me.
Reclaimer Dragon (Wild ARMs 4) vs Lenneth Valkyrie (Valkyrie Profile Series): Lenneth absolutely needs to dodge once to win this. She is pretty dodgy but not sure if it's enough, may look into this more later.
Heavy
Rofel Wodring (Final Fantasy Tactics) vs Justin (Grandia): Justin's best hope is that his weapon is immune to breaking. If not he loses instantly. If that's the case, Rofel breaks his armour first to lower his damage, then something else to finish the 2HKO. Justin could come in with no equipment, but... surely he still gets 2HKOed anyway, and also has to worry about status. And I don't see one unboosted H&E Cut as one-shotting Rofel.
Athos (Fire Emblem: The Blazing Sword) vs Marle (Chrono Trigger): Luna 2HKOs and Marle can't survive the eventual crit. Her only hope is to status first, but Provoke can't be doubled and either has to contend with Athos' awesome Res or his decent evade, and has to be constantly reapplied. I think it's too much.
Alfina (Grandia III) vs Arnaud G. Vasquez (Wild ARMs 4): Kneejerk is Slow Down keeps Alfina from really taking advantage of Stun Force at all, and Armageddoning instead still leaves Arnaud with the edge speed-wise... but she blocks his ID/sleep bullshit so he has to kill with damage which is very slow after Armageddon. But eh, Armageddon wears off and I have to think speed makes up the difference of any damage.
Middle
Khalamari (Dragon Quest VIII: Journey of the Cursed King) vs Cid Highwind (Final Fantasy VII): Has enough damage control to not face a L3, and isn't being outslugged otherwise, I don't think.
Yulie Ahtreide (Wild ARMs 4) vs Nowi (Fire Emblem: Awakening): Nowi's thing is being durable, a healer spoils that. Also, Yulie has the ITD Sacrifice, so no dice hyping tinking here. EDIT: Oooh, but she can't use Sacrifice against range 1-2 counters, riiight. Well. My respect for subtraction defence is still lower enough that this isn't an issue, but that is amusing.
Chloe Hurtzog (Mana Khemia 2: Fall of Alchemy) vs Sara (Breath of Fire): Sara can enjoy not fighting healers for now.
Light
Anna (Fire Emblem: Awakening) vs Lucia (Shadow Hearts: Covenant): Lucia can Rage then 2HKO, but that's still giving Anna three attacks even if Lucia never misses. And she surely will once.
Nei (Suikoden III) vs Peppor (Chrono Cross): Speed should let her take this, I'd think. It's possible she even has a 4-3.
Sacred Slayer (Wild ARMs XF) vs Miranda (Grandia III): uhhh kneejerk