IIRC the original design for Vader's ANH saber back in 1976 called for the hilt to be all black.
Lucas probably left the silver accents on Vader's otherwise "black" MPP to represent the hope for his redemption.
the saber in ATOC is anakin's first saber, and I suspect that it looks like the Vader MPP saber for a reason.
as you pointed out, its basically the same design, except for the color.
(more chrome = a lean to the "light side" ; more black = a lean to the "dark side")
I think that was done for symbollic reasons, more than anything else.
----------
as for the saber in ROTS,
it was always doomed to mirror the Graflex flashgun that was used to make Luke's saber :P
I have two possible "explanations" for why the design might have changed, from anakin's POV:
1) there was a War going on at the time it was built. LOL. and who has time to bother with the emitter shroud during a war?
other than that, its basically the same design (same length, same grips) so really there's not much difference. its just missing some cosmetic detail.
that's perfectly understandable during a war.
look at Obiwan's. his is (also) the same basic design that he used before, but its missing most of its 'coverings'. perfectly understandable during a War. :P
2)the mechanical hand. the ATOC and ROTS sabers feel the same in the left habnd, where the grips are,
but on the forward hand (the right hand) its a different saber.
Anakin might have changed his design to accomodate his mechanical hand.
---> his new hand in the suit as "Vader" was more "life-like" and he went back to his original design.