I am a die-hard enthusiast of both brands, but for a duffle bag, I would definitely choose the Filson. The Filson carries essentially the same warranty and is extremely durable, but the big factor here is weight. The Saddleback duffle bags weigh-in at 12-13 pounds empty. When a duffle gets this large, the weight of your clothes, etc. is significant enough without having to add 12 extra pounds to the mix. In addition, I think canvas is sort of what a duffle bag is all about.
For briefcases, I would choose the Saddleback. For messenger bags, satchels, etc. an argument could be made for either choice. But for a duffle...get the Filson.