Next to the amount of PH/
PR going on, the behavior that I saw in individual OOTP games, which bothered me the most, was how runners on 3rd would almost always score on GBs hit to infielders. It did not seem like defenders ever tried to prevent the run in those situations.
Looking at it a little more closely suggested a pattern in OOTP. If the infield played in, the runner on 3rd never tried to advance. If the infield played normal, the GB play was always to the force out (or to the hoped for DP, which was likely set up by a IBB if necessary). There are two exceptions to this: bunts and balls hit to the pitcher with bases loaded.
IRL, runners on 3rd were more often frozen there by infield play on GBs, or plays were made at home more often, than I was seeing in OOTP. I can’t quantify this – it’s just weight of observation. (Note: I have been playing through a 1960 league, game-by-game, and comparing what happens with box scores and game logs from the same games actually played in 1960).
AFAIK, the “Infield In” slider in the team manager pages is the only tool we have to influence how often runners on 3rd get a free pass home on infield GBs. I have been setting this all the way to “frequently” on all the teams in my 1960 league. I have no way of evaluating if this is the “best” setting, or if some place slightly to the left would be better. But, so far, I’ve been unable to detect anything really negative from setting it there. I’m sure there must be some hits occurring that would otherwise be handled by infielders, but it certainly isn’t dramatic. OTOH, it does make scoring from 3rd on an infield GB noticeably less automatic. It also increases the likelihood of a play at home, infielder to catcher, with bases loaded, which happened very, very rarely before.
On a related note: IRL, you see non-force plays made at 3rd or at Home on infield GBs (that is, the infielder throws for the tag on the advancing runner rather than for the force out). Not a lot, but not all that rare either. With one exception, I’ve only seen this happen in OOTP on bunt plays. The exception was a bottom-of-the-ninth, winning run heading home situation. I was glad to see it, because it meant that it could happen in OOTP. But it is much too rare, which does take away some excitement from the game. I haven’t come across anything that an OOTP gameplayer can do to influence this behavior, so at this point it’s just an observation.