My all time favorite Baseball game is Super Baseball Simulator 1.000 on SNES. It's just perfect with crazy assed super moves, customizable teams, arcade style gameplay and season mode.
Then my runner ups are Baseball Stars (NES), Baseball Stars 2 (My Neo CD version), Super Bases Loaded 2 (SNES), Super Power League FX (PC-FX) and World Class Baseball (OBEY)!!
I remember trying some Major League Baseball and Bases Loaded '96 on Saturn, but thought the transition to 3D was pretty rough and it lost most of it's gameplay (Arcade style?) that I loved in my 8/16-bit baseballers. But your post about Bottom of the 9th has me intrigued! I will seek this out and give it a shot!
Thank you,