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Bidding for free agents against the AI (no immediate signings)
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Waiver Wire
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Manager Signings/Firings
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Realistic 40-Man Roster Rules
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Three-way trades
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Enhanced Injury Engine (the ability to play hurt, e.g. "he's at 85%" etc.)
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Stadium improvements (e.g. luxury suites, additional seats)
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Backloaded Contracts (e.g. $3M in 2005, $4M in 2006, etc.)
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Player Hot Streaks. More Morale Depth.
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Editable Number of Pitchers Per Team and Roster Sizes
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Expanded revenue options (merchandise, concessions, media contracts etc.)
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Player-of-the-month (week, game) awards
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Salary Caps and Revenue Sharing
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Team Rivalries (with bean balls, brawls, and related news stories)
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Computer-controlled owner (that sets your budget and/or fires you for poor performance)
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Enhanced Play-By-Play: Triple Plays, Taking a Base on Defensive Indifference, Ejections, etc.
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Editable League Structure, Interleague Play, and Playoffs
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Minor-league TOTALS in Scouting Report
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Schedule Editor
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Playoff TOTALS in Scouting Report
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Rule 5 Draft
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Use a Pitcher as a Position Player or Vice Versa
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Incentive Clauses
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"Almanac" (automated yearly HTML output of all of stats, standings and leaders)
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Other [non-lefty/right] split stats (home/away, day/night, runners-in-scoring-position, month-by-month)
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More severe personality effects (e.g. "clubhouse poison")
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Ability to Move Pitcher's Slot to any Position in the Batting Order
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'History' Dialog lists all franchise years (not just the ones you controlled the team)
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Auto-Sort Button for Strategies
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Inflation (e.g. Babe Ruth earning $100,000 NOT $10,000,000)
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New Screen and Dialog background artwork
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'Team Options' Slider for Percentage of Games to start Alternate Starters
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Computer-controlled commissioner (vetoes cash-only trades, disallows team movement, etc.)
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Improved Sim Engine for Deadball Era (pre-1920)
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Improved HTML output for running leagues
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Team Stats Output - the ability to display, sort and print a range of team stats (not just in Standings)
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Saveable Roster Dialog configurations
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Full minor league teams (with their own schedules and box scores)
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Radio-style audio commentary added to Play-By-Play
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Other (please describe below)