Does Star Ocean 2 count? It was made by Enix, but long before they merged with Square. SO2 won me over with its truly amazing combat and skill/crafting systems - it had (for its time) an interesting plot and good visuals, but more than anything else it really felt like a game from an era where gameplay came first and there was always something cool to do around every corner.
If the eventual Squeenix merger disqualifies Star Ocean 2, then Tales of Graces is my second-favorite RPG of all time, for its lovable characters ("M. Caesar" anyone?) and wonderful action-packed battles. Persona 4, Persona 3, Tales of Symphonia, Dark Cloud 2, and Azure Dreams all have a really fond place in my heart, as well.