I thing that the rule with stamina is good. It makes an obligation for every team to make the substitutes play at least 48 minutes. This rule is the same for everyone and everybody knows it. You can not play all the games with the same team, it makes tactics more interesting and gives a bigger role to the managers that we are...that's why the game is interesting. Otherwise it will be the same every game and every week...and it will be boring!
I see your point, and I agree that it's necessary to increase the role backups play. The problem is the negatives far outweigh the benefits of this rule.
1) As has been stated by others, if a player gets injured for a few weeks his stamina can drop several times. With a lack of individualized training this seems a bit absurd. I can understand a player having a recovery process following an injury, especially one in excess of 4 weeks, but to have to stop everything the team is doing training-wise to get one player back into game shape is a bit much. It just seems to me that every player becomes a time bomb in this current format. Eventually, the transfer list will be littered with players who have good skills and awful stamina because they stubbed their toe a couple times over the course of a few seasons. Give us an option to have players forgo their skills training in favor of stamina training (even if it's at a reduced rate) on an individual basis and this problem ceases to exist.
2) If players naturally lose stamina for not playing enough minutes, shouldn't they naturally increase stamina for playing more? It seems pretty common sense to me. Give players who play enough minutes a week stamina gains. I'm not talking a level a week mind you, but over the course of a season a player who gets a significant amount of playing time should see some stamina increases.
3) Why twist my arm
more? There are already two negatives to playing starters too much: increased chance of injury and drops in game shape.
I think the stamina decay is a good idea in some aspects but it's a bit unreasonable in it's current format and needs another look.