It isn't noticeable using the default textures because the biome colormaps use very subtle gradient, but as soon as you use a resource pack with more radical color variations it becomes evident.
I took 2 pictures in Taiga and Forest biomes and included the colormap used in the RP (Pixel Reality).
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This is arguably desirable in the foliage colormap.
I can tell you, it is not desirable. It looks rather ugly.

Probably the upper block takes another pixel of the colour map due to increased Y coordinate.
Yes that's exactly what it is. And default's color maps are no-where near utilizing the new features with biome coloring, no template was released.
Some artists have already figured out how it works, but that's beside the point, default should always utilize how things are mapped and implemented, not only as a show of good-will towards artists, but also as a show of competency, and that there is actually a REASON it was added that way.
images added
Also, IMO recoloring sugarcane is ugly and just silly >:|

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Still happening in 14w02c
The best solution to this would be either:
use the color from the very bottom of any connected plant (tall grass, ferns, sugarcane)
or
use the the color blended between the existing connected plant, either as a whole or per section. This could mean that a blue bottom and a red top could make a purple plant, or a plant that was a gradient which was blue at the bottom, red at the top, with purple at the middle.
relates to MC-29590
Confirmed for 14w31a.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases. If this has been done, we can reopen the issue.
Keep in mind that the "Resolved"-Status on this ticket just means "Answered", and that we are waiting for further information on whether this issue still exists or not. We will reopen it as soon as the requested information has been deliviered.
No response for over a year.
Confirmed from 1.9 through 1.9.1 pre-3, please reopen.

Changed reporter to @unknown
Added a resource pack (mc_30630.zip) to make the issue clearer. It has both a colormap and double-tall textures. The colormap has exaggerated colors that are can be chosen for each height (which makes the issue much more noticeable, and the double-tall textures are included because dual-coloring looks much worse on cleaner textures that are more unified between the two blocks ('airy-er' textures, especially those with somewhat noisier textures might have the issues be less noticeable).
As with all properly zipped resource packs, simply download the file to your resourcepacks folder and then add it to the top of your resourcepack-stack to see its affect.
It should affect most biomes, the exceptions are those without color variance (I think deserts and the nether fall under this) or those that don't use the colormap (swamps and mesas... swamps DO have color variation but I don't think it's height based, so won't trigger this issue)... roofed forests also only partially use their biome colors, so might only have a partial variance effect.
A good way to see the issue (besides searching for a plains biome or spamming double-tall grass everywhere) is to place 2 grass blocks down (on top of each other)... if the color of the bottom and top mismatch, so will the double-tall [grass/fern] in the same spot.