Well, I was born and raised in Omaha, spent a majority of my life there, moved to Lincoln in 1992 and except for a couple years have lived here since. Let me tell you, there is a HUGE difference between the two. Now don't get me wrong, I like both cities and each has something the other doesn't but I have now bought a downtown Omaha place as our "lakehome"

and that should tell you which I favor.
Why I have an Omaha place and eventually will live there full time:
Omaha has MUCH MORE CULTURE = mostly downtown
Omaha has my beloved Creighton Bluejays
Omaha has my family and so many more friends than Lincoln
Lincoln is amazingly cliquey {is that a word?}. If you weren't born here, you will always be an outsider.
When I first moved to Lincoln, I was early 30's and single. Believe me, there is no scene for early 30's and single. The college scene is great and the retirement homes are superior {I mean that sincerely}. There are good schools and nice neighborhoods. I am now married and that makes things much better but we never had kids so that makes suburban living tough no matter where you live {try listening to cocktail talk next time you're in a group and see how often it turns to the kids}. Lincoln is a Grand Island/Fremont/etc except it has the state university and government. READ: small town mentality with the issues of smaller communities {ag, etc} important here too. If you get the Lincoln paper, there is little about Omaha and urban but plenty about small town issues. Also, if youo want to talk Husker football 365 days a year, come on down.
Bottom line, I am here due to an awesome career opportunity. If you have a spouse, 2 1/2 kids, a dog, two story suburban home and a desire to be a junior leaguer, Lincoln really is a nice place {WATCH OUT FOR THE CLIQUINESS IN THE BUSINESS WORLD}. You also fit in out is the suburbs of Omaha.
If you are young and hip, if you are old and hip, if you are a childless couple, if you love the arts, if you love big events {college world series, volleyball final 4, ncaa basketball tourney, etc} {first line concerts} {art exhibits} you should live in downtown Omaha, Dundee or the like.