Lyndis (FE7) vs. Titania (FE9/10): Similar enough artstyle, so my own biases towards more mature and buffer make this pretty easy.
Seneca (SuikoTactics) vs. Elena (FF7): Never really seen any terribly flattering pictures of Elena.
Legretta (TotA) vs. Maya Shchroedinger (WA3): Hmm, not bad.
Rise (P4) vs. Rozalin (Dis2): ... Rise? Rozalin? Persona might actually have an artstyle advantage, which is frightening. Still, uh, Rise is at best cute in a little girl kind of way.
Miki (CC) vs. Cleo (Suiko1): Man, CC art, I dig you less and less as years go by, just like almost everything else about you.
Cissnei (FFCC) vs. Tifa (FF7)
Lucia (Suiko3) vs. Emeralda (XG): Lucia is just plain hot, as well as playing to my biases, sooo yeah.
Rinoa (FF8) vs. Heather (FE10): Both moderately pretty. Think Rinoa's a bit better, though. Heather certainly wins personality, at least.
Tethys (FE8) vs. Miang (XG): Miang is among my favourite RPG characters, and while they're not the larger reason, I am not above saying that looks were part of the fanboyism there.
Chris (S3) vs. Refia (FF3): Refia just looks too horrible in-game. Her art's okay, but sorry.
Yuna (FFX) vs. Natalia (TotA): See Miang, although in this case it's clearly a case of the character making me dig the look more, since I don't recall finding her that notable before playing the game.
Tanith (FE9/10) vs. Linde (FE:SD): Hahaha. One of the best-looking FE women (what is it about Begnion pegasus knights?) vs. FEDS.
Freya (VPs) vs. Aelia (VP): You know the story here.
Lethe (FE9/10) vs. Paine (FFX-2): Critical failure. Well, Paine's not ugly even if I don't dig the goth look, but Lethe isn't even hot by laguz standards, since the wolves (and to a lesser extent Tibarn) steal that.
Sheena (ToS) vs. Reimi (SO4): Ewwww, Sheena. Reimi on the other hand is certainly cute.
Judith (ToV) vs. Shanoa (CV: OoE): Need to go relook at Shanoa, I just have vague memories of her from the box art of OoE. Strong kneejerk is Judith, though; she is hot despite the fact she is too good for clothes. EDIT: Shanoa isn't bad, but yeah.