The older single level Comet cars don't have this problem nor does the light rail. Seems the solution is to replace with a longer lasting window material which is already known to work.
That material is glass. However... replacing panes with glass isn't a straight swap of one material for another. The glass has to be protected around the edges, it can't be drilled for screw holes, etc. The re-design involves not just the window material but the window system.