ATL 4 (Bebedora got a specific mention) Abstain
Chrono Cross (Lesser used, less connected, later characters; Split-path characters; Pip and Sprigg) hm. Keep for now. Can I confess I don't want my (kinda but not really) namesake booted? Even though she probably should be?
Baldur's Gate Abstain
Brigandine Abstain
Fire Emblem 7 (Lesser used, less connected, later characters) Abstain
Phantasy Star 1 Abstain
Phantasy Star 2 Trim significantly (just Rolf is fine by me, but more is ok, too.)
Shining Force 1 Trim, but keep bosses/major characters (do I need to be more specific than this?)
Shining Force 2 Trim, same as SF1
Barbarossa (Suikoden) Keep. Call Golden Hydra or whatever if it makes it you feel better.
Suikoden 1 (Lesser Used, Less Connected, Later Characters) Keep non-vanilla characters that may fit that description, boot the rest
Suikoden 2 (Lesser Used, Less Connected, Later Characters) Same as S1
Suikoden 3 (Lesser Used, Less Connected, Later Characters) Keep everyone.
Tales of Eternia Abstain
Valkyrie Profile (Lesser Used, Less Connected, Later Characters) Keep. With a remake out there and sequels to keep interst active, I don't think booting is in order. Besides, unlike Suikoden, VP scrubs are actually usable without too much trouble.