I have read studies that show the minimal impact of various line-ups. That being said, I do think managers must try to make an impact, even if slight, to improve the odds of winning each game. All things being equal, I would do the lefty-righty thing. I never completely wrote off its advantages, but often times, a manager will use the lefty-righty theory to an extreme and place a clearly inferior hitter in front of a much better hitter (either overall, by L-R splits or individual pitcher-hitter splits) just to make the line-up look "balanced". I do not think the advantage you get late in games, when opposing managers bring in a lefty then a righty every batter makes up for the loss you may get innings 1 through 6, 7 or 8, if ever.
Just the fact that each slot usually gets 20 to 30 more PAs over a season than the one below it, makes a big difference. That's why I keep Betts number 1. I don't buy the Pedey is best at number 2 mantra for several reasons, two of which are as follows:
1) He isn't as fast as many think he is.
2) He has actually had better success batting 3rd and 4th (combined) than 2nd over his career.
I'd bat Bogey 2nd, since he lacks the slugging percentage to bat 3rd.
This would be my template for a line-up that does not factor in individual splits vs that days pitcher, recent trends (hot streaks/slumps), injury factors and more...
Vs RHP Vs LHPs
1) Betts Betts
2) Bogey Bogey
3) Ortiz Pedey (maybe eventually HanRam)
4) HanRam Ortiz (maybe HanRam if Papi slumps vs lefties)
5) Pedey HanRam
6) Shaw Shaw
7) JBJ Young
8) Holt JBJ
9) Vazquez Vazquez
I do think the 3rd batter should be your best OPS guy.