The problem is that it's impossible to compare color tones using YouTube clips because their compression process doesn't preserve color fidelity. However, FactCheck.org got hold of a high-quality recording of the ad as it appeared on station KCEN in Waco, Texas, and then compared it to MSNBC's streaming version of the debate from which the clip was taken. Here it is (the ad is on the left, the original debate is on the right):
In the ad version, Obama's face has been desaturated (i.e., there's less color tone) but it doesn't look any darker than the original. Nor has his face been widened to make Obama's nose more prominent, as the original posters also suggested. That was yet another YouTube artifact.
Darkening images is fairly standard practice in attack ads, and FactCheck suggests that the Clinton campaign may have done it here. But if they did, it's pretty damn subtle when you compare the original source material instead of stuff that's been sent through the YouTube mill.
Hillary Clinton is running a rough campaign, and I'm pretty unhappy with some of her tactics, but that's no reason to start hauling out all the old Clinton-hating artillery we came to know and love in the 90s. This ad isn't evidence of race-baiting or anything else. Time to move on.