I am also doing my windows. I have learned through research that Polycarbonate (lexan) is much, much stronger than acrylic (plexiglass), however it is softer so it sratches more easily. It's worth the tradeoff tho as acrylic is much too brittle and will often crack when being drilled and/or installed. lexan has been used to build see-thru snow plow blades and is almost indestructable. You can fold it 90 degrees and it wont crack.
The people who find fault in what you build typically don't build anything at all.