Why do different H+ in polyprotic acids have different K?
You are correct that all of the $\ce{H}$'s in $\ce{H3PO4}$ are equivalent.  

However, once the first H is removed, the remaining two $\ce{H}$'s are no longer equivalent to the $\ce{H}$'s in the original $\ce{H3PO4}$. After the initial deprotination, the molecule gains an overall negative charge making it more difficult to remove the second $\ce{H}$.  Then when the second $\ce{H}$ is removed the molecule gains a second negative charge making it even more difficult to remove the final $\ce{H}$.  Thus, the $K_a$ values for the originally identical $\ce{H}$'s change each time the molecule is deprotinated.