I have been having a bit of trouble adjusting to the new color paradigm, but in the end I think it will lead to the game having a more Final Fantasy feel to it.

First off, most MMOs have color be purely aesthetic. This is not most MMOs. The biggest complaint I see from people is that they don't want FFXIV turning into a generic MMO clone.

In the Final Fantasy universe, color is not aesthetic!

Black Mage != White Mage != Red Mage != Blue Mage

People are crying out for these traditional Final Fantasy job icons, and yet turn around and raise a ruckus because SE actually ties colors to classes?? I don't get it. The whole theme of these classes (EVEN THEIR NAMES) are highly dependent on color.

Even beyond that, there is a clear line of reasoning as to why colors have stats associated with them. People generally liked the dyeing system (or at least SE believed this to be the case, it seems), where you had to collect dyes and add them to gear. With the HQ system, and crafting in general, this means that adding color takes more effort. Should not effort be rewarded? I know that pre-patch, I was starting to see a lot of people in undyed +3 gear, because the undyed version was exactly the same stat-wise, but easier to make.

If you follow this train of logic, if SE makes dyes not affect stats, no one will make/sell HQ versions of the dyed gear. It would simply be more effort for no more reward. Once again, all people would look the same, just in this case undyed rather then dyed.

The only remaining choice is to make changing color such a trivial operation that it becomes essentially no effort to change your gear to whatever you want, whenever, however. This goes very highly against the color-themed classes/jobs that are so central to the Final Fantasy universe, that I'd think that more people would be against it.

Even further, then SE would be spending a lot of time adding in a system that served no actual game-related purpose. I can already see the cries of "SE, stop wasting time adding stuff to let people play dress-up, and put in REAL content!!".

SE couldn't really win here. No matter what option they took, there was going to be an outcry:
1) Keep existing system : "This is too complicated, and everyone ends up wearing the same undyed gear. It doesn't feel Final Fantasy."
2) Make colors have stats and class/job restrictions : "I can't make my character be whatever color I want!"
3) Make coloring a meaningless vanity system : "Why are you wasting time on a 'Hello Kitty' dress up system instead of adding real content? Why are the Black Mages dressed in red gear and Red Mages dressed in black gear? This makes no sense and isn't Final Fantasy!"

Good luck dev team! /salute