Well the shift rules are in the game. If anything, the CPU doesn't shift enough. And that does impact the game. As would the pickoff move rule (that should be in imo).
But with the clock, there's no way to really make it authentic. For one, the game typically cuts out the pitcher getting the ball. So they'd have to add that back in and/or have the clock start at a different time (since you can't really make players always have to go through that animation; you have to give the option to skip that). They'd have to have the clock on the scorebug at all times (which isn't how most broadcasts are doing it), because the physical pitch clock in the stadium wouldn't be visible to people using the default pitching cameras (by design; MLB didn't want the clock visible on broadcasts).
I'd be all for adding the physical clock to the stadiums, even if they're not actually counting down. But even from an authenticity standpoint, I don't think adding the pitch clock as a mechanic benefits the game (and would certainly take a lot of work to implement, which means something else is getting minimal attention or skipped outright). Same goes with the bases; I don't think the juice is worth the squeeze there, I think that's something that gets touched on when they go back into make foundational changes to the engine (which could be next year if they're dropping Xbox One/PS4/Switch).
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