Every mod combination can give little bonuses:
Shielding:
Shielding + Stealth = +3 max health
Shielding + Hydrualics = +1 block safe fall distance
Shielding + Building = +10% block strength
Shielding + Kinetic = -5% self explosion damage
Shielding + Speed = +2% movement speed
Stealth:
Stealth + Hydrualics = -5% footstep sound
Stealth + Building = -10% building sound
Stealth + Kinetic = -10% explosion sound
Stealth + Speed = -8% footstep sound
Hydrualics:
Hydrualics + Building = +10% jump height
Hydrualics + Kinetic = -5% mid-air damage taken
Hydrualics + Speed = +5% jump height + +5% speed
Building:
Building + Kinetic = +8% block strength
Building + Speed = -5% building cooldown
Kinetic/Speed:
Kinetic + Speed = +10% fall speed
With this system some modifications like Stealth probably will be more usefull. And of course these are just my examples for explaining synergie system better.