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I've never noticed the lineups being too strange when the AI substitutes for my players, but I have to say I've not paid a ton of attention to it.
One thing I do is set my subs to play on a fixed schedule ("every 2nd game, every 3rd game, etc") because that lets me control how often they appear, rather than just letting it be "when starter tired" which is whenever - though I did read on the boards here that left to their own devices, a player will play in around 150 games, taking the other 12 off due to fatigue. So it looks like a sub will play around every 11th game automatically.
As far as the "every 2nd game" settings for the vL and vR lineups, I have always assumed it means each lineup operates independently - so a guy set to start "every 2nd game" on the vR lineup would start against every other RHP - against LHP the vL lineup would determine whether or not a player plays.
Also, I have not tried this, but I have heard on the boards that you can get more control by using the "7-day lineups" at the end of the lineups tab. I believe it uses the exact lineup you specify regardless as to the player's fatigue, etc. However, I've seen people say you need to be careful when using that, because if you don't reset the 7-day lineups, you'll use the exact same lineups the next week (and I suspect with a 5 man pitching rotation, the 7 day lineups would screw up your rotation). I also don't know what happens with the 7-day lineups if you have a day off - say you play 3 days and have a day off. I have no idea what lineup is used the following day.
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