Nowadays I don't think it's that big of a deal. A few years ago I bet a lot of people would say the fleshtone figures look strange, partially because only one or two fleshtone heads would appear in a film. But now with the huge amount of IP LEGO sets, everyone has access to a huge range of fleshtone figures.

With the inclusion of fleshtones, you have the opportunity to make some stylistic choices that you didn't have before with just yellow heads. For instance, for my film Driven, I intentionally chose to use only fleshtone heads for the characters in the dystopian society, and only use yellow heads for the people outside of the dystopian society.

Fleshtone is just another color, and your use of color could turn out to be very important to the look and story of your film. If you do choose to mix the colors but not have any significance associated with the yellows vs flesh, I would try to achieve a rough 50\50 balance of fleshtone and yellow onscreen, otherwise audiences may misinterpret the stand-out colors as significant.

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Echoing Nathan and Sonjira, I agree that your choice of fleshtone/yellow heads has a major impact on look and interpretation, and doesn't bother as many people as it did once. And, though I personally have a bit more of a bias towards the yellow minifigs, that's mainly because it's the only color that was around when I first played with LEGO, and since most of my series tend to feature classic themes (Adventurers, Alpha Team, etc.) I keep an "all yellow" cast to evoke nostalgia.

However, if I did something like, say, a Batman and Superman film, I would try to embrace an entirely "flesh toned" cast.

It really just depends on how you intend to use your figures, and what your story calls for. I didn't even realize the varied cast in Driven until Nathan just pointed it out. But, it's not that the effect didn't work - quite the opposite. It was so well crafted, I didn't even notice the difference, as, it was just a single element to give off emotion, and show onscreen the differences between the "society" and the outside world.

I personally am a die-hard yellow head lover, but flesh heads have there place. To me flesh heads look best in movies taken off of LEGO brands, such as "Batman" or "Star Wars" films. So if I were you, I would keep them separate. But in the end, the face does not effect how like a movie.

For the non-purists out there who like a flesh head but want it to match other yellow heads in a film: applying yellow sharpie to a flesh-colored head can result in a very close match.