Those abilities really matter from a GP perspective. A maxed three zeta, six ability toon (CLS, JTR, Revan) is worth about 9k more GP than a maxed three our four ability toon with no zetas (Spy, Soldier, Sun Fac). GP is taking those differences into account. My CLS and Revan are worth the same from a GP perspective as your Spy, Soldier and Sun Fac. Conversely, I spent 120 more zetas, 280 more purple mats and 33 more omegas on that GP, which you could have spent on something else (and you also got to breeze through all of the new ship table hard nodes while I still haven't 3-starred them all!!)
I do agree that having character GP from crew members 'double counted' in some fashion puts those who have heavily invested in ships at the expense of squad only characters at a disadvantage in game modes that include squad only characters.