Some extra neat features some take for granted:

-See box scores for any game (On the pause menu)!
-Broken Bats... I love watching Lieberthal smacking broken bat HR's :)
-Weather. The weather effects the ball, and nothing beats playing a game in the snow.
-Chicago Cubs fans throw visitor HR's back on to field.
-Over 70 Injury types.
-Computers steal bases. (Overall upgraded AI)
-Pitcher and batter ejections (Batters charge the mound).
-Going....Going...Gone! Press L1 at the end of the day of games to see who hit home runs that day and their current total!
-Wrinklies: Parody of Triple Play
-Pixels: Parody of High Heat

-Accessories
-Broken Up Double Plays
-Comebackers off of the pitchers gloves
-Special stadium effects
-Slide step, pick off move out of windup
-Variety of 1st baseman catching animations
-Overthrows
-Pitching history (I love this feature :)
-Bare handed toss's.
-Intentional Walks, Dropped 3rd strikes
-Commentary (during replays, etc.)