The skills you acquire through getting skill points and supplies along with having a high enough level to even access them should've been made where they are much more difficult to obtain and keep.
1st. The leveling cap should've been made where it seemed almost improbable to reach giving you the sense of progression no matter what.
2nd. The skills in the skill tree should've had power levels going to 100%
3rd. These skill power levels should be made to fluctuate according to your efficiency of combat playstyle.
3A: Stealth skill power level would fluctuate depending on how efficient you were at not being detected. Higher stealth skill the tougher it is to be detected.
3B: Accuracy skill power level would fluctuate by how efficient you were using your weapon: shots hit/missed being your accuracy of course.
3C: Damage resilience power level could be determined by hand-to-hand kills encouraging you to move in close and get those takedowns.
3D: Drone skills would fluctuate by actually using the drone's spotting, emp, explosive, noisemaker, etc. The more you continuously used these drone skills the power level would increase for each individual drone skill.
If you slowed up on using these skills or became inefficient at accuracy or stealth your power level for the associated skill would decline. This approach of having your skills be more involved directly with your current efficiency of playstyle makes every engagement critical to your next. The skills should have never been a static acquired and completed type of thing. Please Dev's take this advice if not for this current game, but future games, possibly an open world Splinter Cell.