You make a lot of interesting points with frequency analysis, but these facts can be used for your benefit.

For example, if you're concerned about transit systems being used to identify you, try leaving the devices in a safe location for several hours and have them respond on a timer system. Any analysis ran across millions of users will end up filtering you out, lowering your own suspicion factor and increasing the adversaries uncertainty when facing big data.

How a system fails is just as important as how it performs when it comes to security, the young-adult novel Little Brother by Doctorow goes into this in good detail.