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I'd argue that a cost efficient organization doesn't only look at the amount spent per wins or per statistical output in the present, but it projects for this cost to be the same or lower in 3-5 years too (or perhaps even moreso). The salary screen should be your bible.
I do always try to be in the bottom third in the league in term of payroll like Brad K. This allows for money to be spent on scouting, player dev, the draft and IFA, which are crucial. I also try to always get cheaper, since this pretty much always mean younger.
A cost effective organization will, in theory, never need to rebuild since it will never get bloated to the point of needing a rebuild. Being as cost efficient as possible is more of an art than strict number crunching imho. A few easy pointers though :
1. Extending or not extending players long term : this is the first thing many teams get wrong. Franchise cornerstones (real ones) can be extended long term at a high AAV but I try to have at most two of these contracts at any given time. On the other hand, if I can get a player to sign a nothing deal long term when he is young, I'll jump on it since the contract will remain tradeable even if the player gets injured or slumps.
2. Free agency : most years, I do not sign any free agent. Free agency is to patch holes with cheap guys or acquire franchise players who you cannot trade for. This is again where many teams fail : instead of trying to trade for a AAAA guy with options on the minimum, they'll sign some overpaid 33 year old vet to be a backup outfielder. Don't do that. Try to be as deep as possible in AAA so you won't have to sign guys in free agency.
3. Every player in an asset/trade chip : don't be afraid to trade away players when they still have value (1-2 years of team control) or when their options run out. This is especially true of pitchers. Always strive to get younger.
4. Give your guys a shot or trade them : it comes a time between 22-24 year old when you have to make a decision. Either the guy gets a shot and possibly becomes a regular, he becomes depth or he is a trade chip to be traded when his value is still high. This is especially true for guys in the top100 prospect list. There's no point in hoarding blocked guys when they still have value or prospects who are highly valued but have lackluster statistical output in the upper level of the minor leagues. They will only wilt and you won't get anything for them.
5. There's value in older guys too : older guys, especially pitchers, who you can get for cheap or even for free, can be recycled as stoppers or even as closers.
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