I agree with you! Although I understand as to why some sets have multiple cross-over skills in there 6p bonus (mostly there), it in my opinion ultimatly doesn’t reward experimentation.
It rather forces us to play “best in slot skill” for those multiple sets (i.E Hungering Arrow for multiple different DH sets as many of them have a generic primary dmg multiplier on there 6p).
It would make more sense for each set to be a distinctive Identity and boost one maybe two skill combination at best without overlapping, this way every set feels unique enough to at least give all of them a try.
Every character class has at least four primary skills and four secondary/tertiary skills. Using the monk as one example of seven, if they did make them usable only in one set, one to TR, one to Mystic Allies, one for WoL, one for LTK, one for only primary skills - They already have done it with ROATS with dashing strike and primaries being the only skills that do any damage. Every class has a similar facility to make a skill viable. Unfortunately, the way they have done many green set builds, skills that should be useable are not an option above GR100 as they simply do not do enough damage.