I'm surprised Fire Emblem hasn't been mentionned yet. Basically this game invented the tactical-RPG genre altogether. Sure by today's standard it's completely un-original because the concept was re-used to death, but back in the day moving your units on a chessboard and alternating between player and computer turns was a brand new idea (I guess).Intelligent Systems made Famicom Wars two years earlier. Fire Emblem was kind of like if they took that earlier game and added RPG elements.
Also, I haven't actually played the original Famicom Wars much. Did it have a "story" mode/ending or was it just single matches vs. the CPU or another player?