For me, it's the matter of originality. I had a nice talk with Mick Gray about this at a signing. Apparently, someone had tried to convince Mick to ink over some pencils Jack Kirby had done. Mick, bless his soul, refused outright, asking him to at least consider scanning the pencils if he really wanted them inked (i.e. he'd ink over the scans, like a blueline). Well, the guy seemed to take it personally, and went off to find someone else to ink over them. Hopefully, nobody agreed.
When it comes down to it, coloring over inks or inking over pencils might be more aesthetically pleasing to you, but that also eradicates any aesthetic value the piece had before the additions, not to mention the ability to look at the piece "before" it was colored ... especially if it's by someone like Jack Kirby. It's the same reason why people will still buy black and white versions of covers, even though a colored one exists.