For realism, I recommend Out of the Park Baseball 6.
The game is so detailed, it's sick.
After trading deadline, players must clear waivers if you want to trade them.
Single A, Double AA, and Triple AAA minor league teams.
Rule 5 draft.
And then are the things that make the game fun and interesting while being rare enough that it seems realistic
Players have a national and local popularity rating.
Rain delays and double-headers.
Japanese and defected Cuban players entering the league before free-agency.
Off-season and spring training injuries.
Player personality. Some players want to play for a winning team, some are greedy, and some simply hate your organization.
Bench clearing brawls and ejections.
Players sometimes come out of retirement and start a comeback.
Play enough seasons and you will start to see Randy Winn Jr., Roger Cedeno Jr., etc. No guarantee they will make it out of the minors though.
Game is $20 and the expansion pack is $10.
"And so he spoke, and so he spoke, that lord of Castamere. But now the rains weep o'er his hall, with no one there to hear." - The Rains of Castamere