Not too sure about the name changes:
Pluto - Charon:
I see nothing wrong with Pluto/Charon's name being Pluto, and in some ways it seemed to make better sense then Charon. First off, Charon sounds like a girl's name (though in mythology it was the name of the ferryman of the River Styx, which makes me ask why they have Pluto's name changed from the god of the dead to a servent of the god of the dead while all the other Commanders got to keep their names). Anyway, since Pluto/Charon was added in Platinum and you don't battle him (he's more of a scientist), Pluto seem more appropriate since Pluto was a planet that got downgraded to a dwarf planet, which seems similar to how we (or at least) I view Pluto/Charon: he is a Commander yet doesn't have the seniority as Saturn, Venus, and Mars so gets downgraded by them in a way. Also Pluto is better well known then Charon, though both Pluto and Charon are considered double dwarf planets.
Handsome - Looker:
I always thought Handsome's codename was strange, and though Looker makes a little more sense I think the name could have been better.
Torn World - Distortion World:
Distortion World isn't that bad of a name, but doesn't really roll off the tongue as Torn World.