I also live in Omaha and commute from Midtown to Downtown daily. Where do you work that they match your bike cost?? That's awesome!

Internal hubs are fine, but at least on my commute, I like to have all my 18 gears.. I hit a few mean hills around Hamilton and California and I don't know how strong you are, but I need them!

You've listed some nice bikes, I would take a look at a few Surly models, the Long Haul Trucker or the Cross Check. I've had both. Currently I ride a cross check with 32 tires and fenders and a Tubus rack with Ortlieb panniers. I probably have less than $1k in the bike and 300 or so in extras. I can run road tires, commuting tires, and fat tires, or cross tires on this bike. Totally versatile.

Good luck, let me know if you want to check out my setup sometime..

Tim