What the meaning of runes, when they run out of use?
My 5 Planeswalkers are all 50’ level.
Apparently the new release is going to have new Planeswalkers and raise the level cap to 60.
This is a long-standing debate. 
They are used to upgrade planeswalkers. If your planeswalkers are maxed, then save them for the next update to apply towards new planeswalkers. Those are the two choices currently available.