I love the idea of this format. While I've never tried it, I've brought it up to my league a few times, but never gotten enough support (or felt strongly enough on my own part) to push it through.
It seems to me that any league could be set up this way, with the ONLY change being that lineups are best ball, rather than rigid.
In this type of scenario, it seems to me that there are only two plausible complaints:
1) That best ball takes the strategy and skill out of setting lineups.
Rebuttal: This argument can only hold water if we agree that setting weekly lineups successfully can be attributed to skill rather than luck, and if it can be attributed at all to "skill", whether or not that skill should be rewarded. Let me explain:
Evidence from my 2007 dynasty league indicates that coaching efficiency is not an indicator of success. Some of the best teams in the league had very low efficiency ratings. Some of the worst teams in the league had the best ratings. While it's a small sample size (12 teams), coaching efficiency appears to have little-to-no bearing on team success. The team with the second most potential points for in our league (1738) had the worst efficiency rating (76.9%) and the most bench points (1367). The team with the highest efficiency rating (87%), had only average potential points and SIGNIFICANTLY fewer bench points (742). Both teams made the playoffs.
Based on the evidence at my fingertips, it could be very reasonably argued that teams with better depth will generally have lower efficiencies than teams with less depth. if you think about it, it makes sense. If I have only 8 solid starters on my team, and the rest is garbage, I can essentially set my lineup at the beginning of the year, let it roll and achieve near 100% accurancy. A team with 16 solid players is going to experience more fluctuation, thus a lower efficiency. We can be debate whether a shallow team with 8 no-brainer every week starters is "better" to have than a team with a lot of depth. But I don't think it can be debated that it takes more skill to put together a team with great depth than it does to put together a team with little or no depth.
In conclusion, it would seem that any reliable measurement of skill related to coaching efficiency is relevant only to the degree that the owner has drafted a team with more or less depth. Whether or not drafting a team with more, or less depth, takes more skill is debateable, but my argument would be for rewarding depth, which lineup submission does NOT do.
2) That best ball reduces the enjoyement of the game by removing the fun out of weekly submission.
Rebuttal: To me, this is almost a case of arguing to do something just for the sake of doing it. If we agree that submitting lineups successfully does not necessarily measure fantasy football acumen, and concede that, in fact, it may unjustly punish or prevent teams from drafting for depth, it forces us to ask ourselves whether or not the act is beneficial. If the sole response is "for fun!", I ask how fun it is when you deliberated for days on two similar players and choose player A, only to have them come up injured in the first quarter while player B would have scored enough for you to win your matchup? Not fun.
One other thing that comes to mind that hasn't been mentioned is realism. To me, the more FF can emulate owning/managing a real football team, the more enjoyable it is. In a real game, if a player were injured or underperforming, the coach would call on a backup to replace him - thus utilizing and being rewarded for depth. Most lineup submission leagues are essentially the same as that coach saying, "Bob's hurt? Oh well. Too bad we can't play Jimmy until next week! We'll have to play without a RB for the rest of this game."
