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Originally Posted by dc_denizen
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I'll concur with your thesis. I think the reasons why vary. Part of the reason may be that smaller cities in NE/IA/MO/KS don't really exist in the shadows of larger cities that they must compete with (Missouri may be the exception). Thus they are the ones attracting regional business rather than losing it to a larger city up the road.
Omaha, to be fair, is far above the 150,000 population threshold given by OP and the other small cities you explored with its ~950,000 person metro. Being the terminus for the transcontinental railroad helped lure industry back in the day. While much of that was tied to agriculture - the city had the world's largest stockyards for awhile - it has somehow managed to diversify over the years into mainly white collar industries like insurance, banking, telecommunications, and engineering. What's left of the ag industry is largely front office stuff for supplemental industries like grain trading and transportation companies. Manufacturing industries that dominated the eastern midwest didn't spread into the upper plains much.
Lincoln's vibrancy is helped by the fact that, similar to Austin and Madison, it is both the state capital and a college town. Lincoln's been doing a lot recently to increase its urban footprint. Within the past 10-years it has added about five blocks to its downtown, transforming what was a large field between railroads:
https://goo.gl/maps/Tz16pDqtj5unwk3s5
...into a bunch of mixed-use midrises:
https://goo.gl/maps/fa6S3Qj2hzm6T96s8
Ames is an interesting case in that its Campustown neighborhood next to Iowa State University is more densely populated and vibrant than its downtown. Downtown has more of its historic building stock intact than Campustown and the architecture isn't cheap-looking, but few buildings downtown are taller than two stories. Campustown on the other hand, has many mid-rises:
https://goo.gl/maps/DCRBjzoWnkHnAuEK9 Of course it's all college kids in Campustown.