Though I have been injured quite a lot over my career, I have been very healthy over the last 8 months (knock on wood). The two big changes that i have made in this time period that have really helped me are these:
1. A bunch of people have said this but REALLY, easy days easy, hard days hard
-you don't get better from the workout, you get better from the recovery from the workout
2. Lift weights. I don't mean do unweighted squats. I mean really lift weight. There's an adjustment period, but i noticed that not only did I recover better from workouts, but my biomechanics improved tremendously as a result. heavy weighted squats, deadlifts, lunges, rows, pullups, bench, shoulder press.