You can modify the XY-Graph in Simulink R2016a. The XY graph that we see is a s-function. If you right click on the block and go to Mask -> Look under Mask, you will see that the s-function "sfunxy.m" is used.
You can modify this s-function according to your requirement. For example, you can clear the graph periodically or provide a marker for the head of the graph. The s-function uses MATLAB syntax, so you can use all the available properties of a MATLAB figure.
Another much simpler workaround would be to use a MATLAB function block. It is fairly straightforward to write to MATLAB function block to plot a x-y graph. If you are not much familiar with using s-functions, I would recommend to use a MATLAB function block.