New features were implemented for Microsoft Windows, Xbox 360, and PlayStation 3 versions. Pitching had been simplified from 2K8 to "2-step pitching", with "hold and gesture", eliminating the third "Release Timing" step of 2K8, simplifying the motion while retaining the style. "Meatballs" (mistake pitches) have been removed - instead, badly released pitches will be less effective (fastballs will be straighter, curveballs will hang, and so forth.) The AI's pitch selection was also improved. (Players may elect to use the third step as an option, and users may also still use the older Precision Pitching from 2K7.) "Influence hitting" allowed users to control fly and ground balls, and bunt with improved precision. The developers added a zone hitting feature, improved hit distribution, and improved fielding realism and AI. Also added is the ability to cancel a throw and hold the ball, or pump fake during a rundown. A player can also attempt a "Quick Throw" which gets the ball to a base faster but also increases the chance of an error. Baserunning control has been simplified; a player only needs to hold down the trigger until it vibrates, for instance, then release it when ready to attempt a steal. There are also separate "Steal" and "Speed" ratings for runners.
The ballpark realism has been changed as well. Players graphically move from the dugout to the batter's box, from the bullpen to the mound, warm up by throwing around the horn, swing the bat in the on deck circle, run out to their positions, and so forth. Umpires, ball boys, and coaches will perform their actions, while fans react realistically. For example, foul balls will cause people in the crowd to jump out of their seats and try to catch the ball, however some fans that have no real chance to get the ball will make a foolish jump in the air. Stadiums will have their unique fan signatures; for example, Turner Field will have the Tomahawk Chop while Tropicana Field will have the Cow Bell. Players will react properly to such events as a walk-off home run, a no-hitter or a World Series celebration. There are also 300 new Signature Style animations. Rain delays have also been mentioned. Arguing with the umpires is not featured in the Xbox 360 version of the game or the PS3 version
The game also had "Living Rosters", active rosters that are automatically updated when the user logs in online; players' ratings will be constantly updated, while up-to-date trades and acquisitions will be reflected in-game. Living Rosters are not active during Franchise mode, however. The game also features a revamped stat simulation engine for the Franchise mode, while players' career arcs are based on how they play rather than preset stat curves. In other words, in order for a rookie to develop, he must receive playing time - he will not develop if he sits on the bench. An entire season can be simulated in a matter of minutes. Other improvements to the Franchise mode include adding a new revamped trade simulator and over 200 individual MLB.com headlines. 2K9’s franchise mode allows for 30 user controlled teams. The mode also has added stats; for example they have included wins divided by teams' payroll.
The game has been updated with an MLB.com-licensed in-game "Virtual Director" website featuring a presentation style similar to NBA 2K9, where the user may check up on league events, trade rumors, player and team performances. The game has improved upon 2K8's Inside Edge scouting system. The game boasts a new level of CPU customization, multi-player functionality, and real player ambitions; for example, Milton Bradley can decline a contract because of lack of playing time, not for monetary considerations. Record-breaking and milestone performances, whether single game, season or career, are acknowledged with headlines and snapshots of the event. There is also a new gameplay mode, "Playoff Mode", in which the user only plays in the postseason. The PC version, like its NBA 2K9 counterpart, will not feature online play or Living Rosters. Unlike MLB 2K6, 2K9 will not feature the 2009 World Baseball Classic.
In other improvements, users can now add SFX and graphic overlays to in-game replays to create highlight reels, as well as upload the reel to 2KSports.com, while online users' performances are graphed out, displayed in chart form, and can be compared against league averages. The Topps Trading Cards system from 2K8 has been improved, while the Home Run Derby mode has also been revamped. Unlike the previous MLB titles, there are no pre-rendered cutscenes; all cutscenes are done in real-time with in-game assets.