Classic lineup theory says your leadoff hitter should be a speedy guy. I disagree. The biggest advantage of Speed is staying out of double plays. Leadoff hitters have the fewest double play opps by far. So my leadoff guys have high Walks and high stamina. Unless he has a ton of Steals at a high success rate, which is rare; Walks have considerably more value when nobody is on base. And stamina is always a factor in the Sim. I'll bat Babe Ruth 2nd or so because most versions have high PA and I don't want to waste them. 4th or 5th belong to hitters who might need some rest.

A mediocre hitter with great glove should bat low to keep him in the field for more games. Tony LaRusso's nonsense of batting the pitcher 8th was all about boosting Mark McGwire's stats. But in the Sim it matters if you have fatigue issues. Low caps sometimes bat the pitcher 1st to preserve stamina, at least early in the season where it has a greater impact.
L/R strategey changes depeding on whether LP or RP is startong. They'll change pitchers midgame but the early guys see the SP more often. And lineups may rotate L vs R because RP are chosen based on who is coming up next but that is not a major factor..