The primary problem is that CPU can react bizarrely to good players being left off of the 40-man. Injured players can take over a year to be promoted back up to the bigs, even superstars. The root of this problem is that the CPU is incredibly cautious to put new players on it's 40-man roster. Players can also entirely disappear in RTTS, though I'm not sure if that's still an issue this year.
Another small benefit is that it's simply a more realistic experience. Teams will have to carefully consider call-ups compared to when they have 15 open roster spots, since the move can have long term ramifications on the franchise. Plus, teams will have to deal with the consequences of bad players stuck on their 40-man roster. That sort of thing.
There's probably some other reasons I'm forgetting but that's the gist of it! It's always a highly requested version so last year I decided to give it a shot, and they get a decent amount of downloads so I figure there's gotta be an audience for it.
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