i think that you should reset every thing at the end of season..
every time the season ends :
players get 100% health
players get 100% moral
no injuries from past season

because in real life u have a 3-4 months between seasons (thats a long time to heal and to get moral to next year)
you can keep the yellow and red cards.. just like in real soccer

that way at the and of the season you can train all the players harder.. so they have a little bit more skill next season

that is the least you can do for all of us managers.. after you give us 3-4 injuries a week (most of them for 5-6 days)