Please take it for what it is, advice from a wannabe SEO.  I'm basically a newbie at it, but here's what I think:

Use directories, not sub-domains.  Sub-domains basically tell google to separate everything.  They work well for people that have user generated content, like wordpress.com because if one user posts horrible dupe content with pages of links it doesn't hurt the whole site.  On the other side of things, that subdomain does not get favoritism from google because it's on wordpress.com...

So, for your site, I'd recommend against sub-domains.  It's pretty, but it doesn't bode well SEO-wise.

Also, dont forget to 301 those domains to the appropriate URL when you change things up

Subdomain will receive less authority because example.com/omaha will receive some benefit from being in the parent domain.  Are you saying you want to get rid of the domains that have been in place for several years?  What are you wanting to accomplish by switching these sites?