Well, At Least The Guys Are Asian

The appearance of some negative characters in Anime as clearly Japanese while the others might have a more cute or generic look, maybe Caucasian, is striking. I've seen less of that and hopefully the evolution will continue. Remember, American movies and TV shows have a pretty strong presence in Japan and that might be an influence. I think Frozen was the top grossing movie in Japanese movie history. (I read one reason for the evolution of the British accent are American movies and TV.)

Anyway, the characters in Momo looked more Japanese so that's good.

But look how many people in American movies are Hispanic or British doing an American accent. They're all very thin and attractive. We see so few obese people in American movies and America is crazy with obese people. I'm a fat guy so I can talk about it! You got 88 minutes to tell a story so you have seconds to establish characters as good thus likable or bad thus reprehensible. Everybody's trying to make the cutest impression possible.

I think you are, understandably, looking at this from the perspective of a culture that seems rather preoccupied with race. Were there any institutional racism or cultural bias at work in anime character designs, I would expect it to result in fewer caucasian-looking characters, given Japan's historical relationship with America and isolationist tendencies. I can't claim to have a definitive answer, but I can at least provide an alternative viewpoint (… and apologise in advance for a longer post).

Traditionally speaking, in Japan and some other nearby countries, tanned skin is associated with lower castes and paler with upper ones. In India you have more ethnic diversity which plays into this, but with Japan I've heard the association stems from the days of yore, where those working (tending crops in fields for example) would brown in the sun while the nobility could stay cool and milky-skinned indoors. So the result is lighter skin tones have connotations of purity which incidentally lends itself to female characters, and conversely the 'bad guys' will often be darker to make things clear for the audience by contrast (echoing ghoolsby's last point). So one might say the pro-lighter skin trope pre-dates Japan's interaction in earnest with other cultures (1860s onward).

Big eyes are an undeniable trend, but like the slightly upturned nose-points, it's one just as well attributed to an inclination towards all things kawaii than an attempt to whitewash character designs. Practically speaking, larger eyes can make facial expressions simpler to animate and easier for the audience to read (particularly for TV anime in the era of smaller screens).

I think the character style in Momo is largely neutral rather than being more caucasian than asian (similar to Ghibli films in that there's not much difference between the european characters of Kiki's Delivery Service and the japanese ones in most of their other films). The side effect of fewer recognisably asian features is that they become more open to interpretation and cultural bias. That said, the films are made first to appeal to a Japanese audience accustomed to certain character styles, and audience expectations play a big role in most major films.

Also interesting to see Tokyo Godfathers mentioned, as Satoshi Kon consciously favoured character design that was more realistically proportioned and recognisably japanese- particularly with smaller eyes than many anime characters. For example, I'm half japanese and I recognise my own cheekbone structure and slightly slanted lower jaw in Hana's character design (the lipstick, not so much). However, I think the leader of the similar gang of punks in Perfect Blue sports the slightly darker skin tone, plus a pretty uncouth manner of speaking that seems to fit the class connotations I mentioned above. Shonen Bat in Paranoia Agent, another darker complexion, so read into those what you will.
And to ghoolsby, in the interests of a fair test, I'd say there weren't any antagonists in Momo- if there had been, the director might have made them very dark and even more japanese-looking!