The likes of Star Wars & GI Joe work better at the smaller 4" scale, due to the vast number of characters & the huge role that vehicles played in their stories.
It really depends on the type of theme/gimmick the property has, and what kind of characters are featured. Fantasy & monsters I feel usually work better at a larger size. Whereas with space & military themes I generally prefer smaller figures, so they can ride in spaceships & jets that aren't too big to fly & swoosh around a room.
Most of the toy companies prefer the smaller scales nowadays as they are cheaper to produce. Price point is also very important to consider. The larger the figure, the more expensive it'll be. Most modern 6" or 7" figures are aimed at adult collectors.
If I was designing an action figure line i'd probably go with 6" scale, but if the line was to heavily feature vehicles and playsets i'd definitely make them smaller.