I posted a comment in GA mega, and posted here (pending approval). My take on this is that that GP is bundled rather than matched on separate criterias of Ship GP and Toon GP. Also, ship GP is overly inflated in comparison to Toon GP. In a competiton thats based heavily on characters themselves while pairing based on GP, a hugely inflated ship gp(counts for roughly 1/2 of a players gp, yet only pertains to of 1/3 GA? and 1/5 of TW event) hurts the players invested in ship arena without rewarding them in PvP events. While players who are not invested in ship arena/ships, have no handicap of this sort in any PvP event.
Basically scale ship GP better, or match on two separate GPs if GP is the matching factor. Its absurd to know that having ships becomes a handicap overall.