Preferably utilizing any fighting game system that isn't Dissidia's.
Cecil (FF4)
Cloud (FF7)
Squall (FF8)
Zidane (FF9)
Tidus (FF10)
Lightning (FF13)
Crono (Chrono Trigger)
Serge (Chrono Cross)
Fei Fong Wong (Xenogears)
Ramza Beoulve (FFT)
Isaac / Felix / Matthew (Golden Sun1/2/3)
Vyse (Skies of Arcadia)
Lloyd Irving (Tales of Symphonia)
Yuri Lowell (Tales of Vesperia)
Yuri Hyuga (Shadow Hearts)
Ness / Lucas (Earthbound / Mother 3)
Laharl (Disgaea)
Hero (Dragon Quest V)
The Nameless One (Planescape: Torment)
Stocke (Radiant Historia)
Commander Shepard (Mass Effect)
Marth (Fire Emblem)
Ike (Fire Emblem)
Tir McDohl (Suikoden)
Nier (Nier)
Sora (Kingdom Hearts)
Minato / Souji Seta (Persona 3/4)
Demi-Fiend (SMT: Nocturne)
Just listed any semi-notable protagonist I could think of (and some guys I just like but whatever). I'm sure there's plenty I've missed. This game can't exist due to the licensing hell it would be, but man, imagine.
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Black Turtle did a pretty good job.