One reason that I can understand for existence of different protection systems for helicopters, large transport/VIP aircrafts/commercial aircrafts and fighters is the maneuverability.
A fighter aircraft complements the flare ejection with a break to right or left.
On the other hand, large aircrafts can't do this. For the flares to be effective, the aircraft should do a break too and this is not possible for large aircrafts. So they are in need to different protection systems like Nemesis.
But this is just one reason.