To avoid having teams with only 5-8 players on their roster you are spot on with suggestion 2. Stamina/Energy depletion.
I also think that Stamina should play a bigger role, and that the energy depletion should be more of a factor.
If you play a fast tactics, your players AND your opponents players energy should drain faster, forcing a substitution more often or a decrease in performance. If a player is forced to play more minutes than he has the stamina for, the risk of an injury should increase. Here the minutes of the previous X number of games should also affect the risk of injuries.
A player who constantly plays 48 min in a fast tactics every game of the week should get a massive decrease in performance and running a very high risk of getting injured.
This might be the case right now, but if so, its not enough. It needs to adjusted accordingly.
This will force teams to have a bench, and a good one if you want to beat the best.
No longer can you win a championship on only 5-6 players.
I agree with you on suggestion 1 too, but only for homegrown drafted players and a small increase in performance.
But why on earth would you like to change the way multiskilled players affect each position? What has that got to do with this?