Stealing Dune's format because I'm lazy. <_<
ATL 4 (Bebedora got a specific mention): Boot Bebedora, keep the rest.
Chrono Cross (Lesser used, less connected, later characters; Split-path characters; Pip and Sprigg): Boot the plotless and bigger pathsplit issues, I'll try and come up with an actual list later.
Edit: From a quick glance at the ranked characters list I would get rid of: Leah, Orlha, Pip, Sprigg, Greco, Janice, Skelly, Draggy, Poshul, Doc, Macha, Funguy, Mojo, Luccia, Neo-Fio, Turnip, Mel, Van, Pierre. Guile is split but he's the easiest to find in my opinion and has other strange plot stuff. Other people are at least important even if you don't get them. There may be others that I'm not sure are pathsplit.
Baldur's Gate: Boot.
Brigandine: Keep.
Fire Emblem 7 (Lesser used, less connected, later characters): I don't see a real reason to get rid of these. Everyone remembers them.
Phantasy Star 1: Keep.
Phantasy Star 2: Keep, I guess. I can't see any reason to boot some but not all(aside from like Rolf) and it doesn't seem that bad except for like Kain.
Shining Force 1: I haven't played these so I can't pick out specifics, but boot optional/plotless characters.
Shining Force 2: See SF1.
Barbarossa (Suikoden): Boot.
Suikoden 1 (Lesser Used, Less Connected, Later Characters): There... really weren't many from this? Can't think of any really worth getting rid of offhand.
Suikoden 2 (Lesser Used, Less Connected, Later Characters): Boot, like CC will look into an actual list later.
Edit: I looked at the rankings and frankly, it's been so long since I played I'm not sure who is and isn't forced anymore.
Suikoden 3 (Lesser Used, Less Connected, Later Characters): I would like to trim a few of these, but not many. Stuff like Kenji that nobody cares about.
Tales of Eternia: Boot Ras and Shizel, keep others.
Valkyrie Profile (Lesser Used, Less Connected, Later Characters): Boot Freya? I can hope, dammit. <_< Keep otherwise.