We recently had to replace our inground pool cover and went with this product:
http://www.glipoolproducts.com/product.asp?ProdID=5
Our pool is not rectangular either... it's called a "lazy L" but we are very pleased. We sent them our old cover so they could use it as a template to custom create the new one. It's very strong and durable and even blocks the UV light that produces algae