Beatrix: This issue is really messy thanks to FF9's damage cap. It'd be impossible for her to break the curve as much as she does early late, which is the problem - in most games, you could assume that they stayed that broken, but FF9's system insures for a fact that that isn't the case. That said I do agree that people should be scaled against the time you face them. FE7's Lundgren is, for his stated level, a total wuss at endgame - but you don't fight him at endgame, you fight him early on. Not sure there is a good answer to this aside from "force Bea to use her boss form."
Cecilia Lynn Adlehyde (WA1) vs KOS-MOS (XS): Inclined to lean KOS-MOS? Cecilia's speed isn't great to begin with and it's getting ruined. Also XS3 KOS has a fairly clean win, I think, Blood Dancer->OHKO and no amount of buffing saves Cecilia from it.
Fayt Leingod (SO3) vs Nel Zelpher (SO3) - I'd just like to point out that "LOL Healing" isn't a good answer here, as this fight clearly takes place in the SO3 battle system and Healing would force Nel to stand still and get smashed by Fayt's attacks. Inclined to think Nel anyway, though - they're both pretty fast at scampering around the field, but I think Fayt's long range attacks or attempts to get into short range (Side Kick) are generally worse than Nel's. She can probably harry him from a distance with stuff like Ice Daggers, while Fayt's Dimension Door or Air Raid is too telegraphed vs. a human opponent who can just run away. (And as for Ethereal Blast, uh, yeah, no, that's not hitting ever.)
Ena (FE9) vs Lucia (Lunar:EBC) - Okay, for the record I voted DNR for Ena, but... if she's using her boss form, there's no way she can move. I know that movement is usually thrown out in the DL, but this is more like "how the battle works." In-game you can slaughter her without ever getting touched, and if there was a boss in another game that couldn't hurt you unless you used short-range attacks, it'd clearly be held against them as well. So yeah. Ena almost always loses against someone with a spammable ranged attack for me.
Except for Lucia. Lucia's damage for Atomic Burn is listed at a mighty ~250 or so damage in the stat topic against an average of 680 (!!). And Lucia's lightning damage is EVEN WORSE than Atomic Burn. I guess you could use Lucia on late Disc 2 and throw out her final Zophar form, where the damage average wouldn't be as obscenely high, and Lucia's damage herself needs to be factored into the new average to bring it down a bit, but the point remains. Lucia can't really do damage. And Ena's resistance is stupid, at least the boss form - good mages like Soren who can do 15-20 damage to randoms can only do 1-3 (perhaps doubled to 6) to her, and if you were unlucky might easily tink. So none of Lucia's damage can even break Ena's resistance, so no damage doubling anyway. If you throw out subtractive defense, then Ena's Resistance is still functionally 80% magic resistance, so Lucia is only doing 1-2 FE9 damage a round - easily soaked by Renewal.
So yeah. Nobody ever does damage. Since Ena is a boss and if you refuse to finish her off in-game, you don't advance, and Lucia is a PC, I'm tiebreaking for Ena here. Fail, Lucia.
Against the PC form (which I never got so I wouldn't allow anyway)... Lucia starts spamming her defense booster. Lunar2 defense buffs wore down pretty quickly, but were awesome while they lasted and stacked, so I think Lucia can survive Ena's assault by spamming healing, with the only worries coming toward the end of Ena's transformation when the buff has declined. Then Lucia needs to actually kill Ena while she's back in human form - if she stalls against PC Ena, eventually Ena will get a crit, or if you really respect the defense buff / disrespect Ena damage, two crits in a row. Problem is, even human Ena has great Resistance (against a higher average though). She probably STILL just shrugs off even Atomic Burn for 0 damage. So Ena wins again, though more cleanly this time.
Also I'm inclined to force Lucia to use AI anyway since that's how she works in-game, which guarantees a loss. (Though Lucia-on-AI needs an immediate downgrade to Light.)
Kornell (G3) vs Caellach (FE8) - Kornell for heavy. Kornell Buster cancels (as does his basic physical). Personally I'd say that this turns off Fire Emblem counters, as in-game a cancel sends the character back to square 1 in which they can't really do anything. Sure something pre-emptive like Hamedo or Flash would beat it, but after-the-fact counters don't seem in flavor. Also I give Caellach last strike since he's another non-moving FE boss, but once Kornell engages then he's normal since Caellach is at least smart enough to have a ranged attack. So yeah, WOW->Buster->Buster. No way Caellach is killing in one hit unless he gets a crit. Heck, Kornell might not even need the WOW.
Eiko Carol (FF9) vs Volke (FE9) - Remind me why Eiko would even bother with Mini? She's got a very very solid 2HKO off Holy here, and even if Volke is doubling, I'm not sure he 4HKOs, which is what he needs. I guess Volke might evade, so sure, Mini -> 2 Holies then, but it seems like Volke needs to get lucky a bit too fast here.