Yes there is a significant difference.
One thing different is MLB13 has a Beginner mode that helps you adapt to the game. It also has MLB Live where you can play the actual games on the schedule with the real lineups as there were IRL as well as a better Diamond Dynasty mode where you can create your own team and player and compete against others.
Not to mention the MLB12 servers are dead so you cant play online or access any of the online features like player or roster vaults or play DD at all.
Thats why MLB12 is only $6