I see what you mean about the differences betwen V2 and V3-a... massively different.
I've not actually noticed any dark lines on the body parts that you mentioned.
I'd say don't fix what isn't broken.
However if you are going to do that, I'd recommend taking an update cycle just to fix that.
I assume it'll take awhile to do them all.
That way you have one cycle of no story that's short, instead of one or more that take much longer.
Either way, good luck!