So give them colourful clothing.

I think that it is possible to make the villagers stand out quite well doing that, rather than give them bright pink faces and red hair.

The thing is, if you wnat the game to be cartoony, then make the background a little cartoony too - more of a cel-shaded effect perhaps.

It probably comes across that I am preferring the 'realistic' look but I'm not, I'm suggesting that I would like to see a more cohesive look.