I am a native of Springfield, Mo and consider myself an expert on this subject. As far as fly fishing goes, I would rather go to a smaller local shop, but if I have to pick I would say BPS carries a few more higher quality brands, but cabelas has a little better housebrand items. So if you know exactly what you want go to bass pro, but if you generally know what you think you need go to cabelas. I disagree with Buzz as far as BPS putting the fly shop in the back, its closer to the front door than hunting, conventional fishing and just about everything else (they remodeled a few years ago). And after all I dont know about fishing in Nebraska, but its pretty good in the Ozarks. I seperate conventional freshwater fishing into two categories (Bass and Other). BPS by far has better and more stuff when it comes to black bass. Cabela's has a wider variety when it comes to trolling stuff, stripers, walleye, and other game fish. It goes the same for the hunting departments. When I am looking for something for deer hunting I look to Cabela's first, but for turkey Bass Pro has worked out better for me.
Another point is Customer Service. I have experienced bad and great service from both. Cabela's once charged me 6.74 shipping on a .99 purchase (I lost some clips on my deer feeder). I called and wanted an explanation and eventually chewed them down to a reasonable price. I got it and they were in a shoe box sized package, and the clips were about the equivalent of a package of size 16 hooks. BPS has notoriously been bad about advertising and fine print.
Also Bass Pro has one return outlet located by its Springfield store, which is good for me, but bad if you dont live in Springfield. Cabela's are located in each the store, which I like better.
Prob a little more than you asked for but thats my .02