Instead of unlocking skills per variant, unlock them per chassis, for the current price. Other mechs of the same chassis, will be able to buy already unlocked skills for the 'respec price'.
There is currently no reason to get multiples of the same mech. The initial idea of the 'rule of 3' was that 'you become more experienced in the weight class/chassis' and thus develop new skills. This could be implemented as a bonus for new mechs rather than a penalty for those you already own by this simple change. If multiples of a chassis become easier to skill, people can more easily get access to specialize in the chassis they like.
This might also increase interest in buying mech packs which come with multiples of the same chassis though it's currently pointless. I've added a poll to see your opinions on this.
EDIT: Due to feedback, I've added two more options to the poll:
"No, Mech Packs need to change" is for people that would rather see the mech packs change from a multiples-of-chassis system to something supported by the skill system.
And of course there's the neutral option, which is similar to the first option, but implies no change of decision whether the skill system supports or doesn't support having multiples of a single chassis. "Yes, though I would buy mech packs regardless" is now for people whose decision would be (partially) impacted by the addition of a skill system geared towards multiples of a Chassis.
I hope this provides you with enough choice.
Edited by Excalibaard, 27 February 2017 - 08:25 AM.