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Secret sauce is secret. For what it's worth, I've noticed that hitting the blue (75%) seems to have a positive impact on team record if not on individual stats. Problem is: that's a team full of Mission Editions, which was good in Diamond four weeks ago but won't do much right now even with a boost. The old Junior-Edgar-A-Rod-Sierra teammate-fest is still workable, but most of the top-notch pitchers are low chemistry...except for Randy Johnson (a bit too homer-prone) and Mike Mussina (insane but probably worth it if you can afford him).
My take is that they set this for theme teams that can easily crank out 85-99% team chemistry due to same team and/or long-term teammates. It's beneficial if you want to run all Yankees or Giants or Cubs or Phillies in a mid-level league, but it won't make enough difference to matter in Gold-Diamond-Perfect now that the Mission Editions are wearing out their welcomes.
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