Brian, nice work and I appreciate your acknowledgement of the comments made here.
I have a few very minor suggestions.
On the interactive map, I would change the legend color from grey to black. Presumably most people initially click on Denver or Milwaukee and it is very easy to associated the result as a Midwest/Frontier color scheme, when it is a direct/connecting flight color scheme.
A cool upgrade in the future would be the ability to click on both a departure and arrival city and see all the different ways of getting there, including Delta and AirTran code shares. (Within reason. Perhaps mileage could be used to limit the code share connections to something reasonable., or whatever criteria are used to actually schedule flights.)
On the static maps, I would show the "combined" map in two colors, Midwest (black) and Frontier (green). For routes flown with a mix of carriers including Delta use blue or grey, or preferably show both airlines in color with slightly different arcs. I realize this is a moving target. The maps should probably also show an "as of" date if the map reflects current routes or indicate an "effective" future date if the routes represent a future route schedule, with a "subject to change" disclaimer or course.
I would think that the Indianapolis and Atlanta code share maps could be combined into one, like the St Paul, Memphis and Detroit maps. Is this not done because the old Northwest is flying out of Indianapolis and the old Delta out of Atlanta (speculating)? I don't see the need to have two separate maps.
The Minneapolis/St Paul, Memphis and Detroit Delta code share map is very pretty, but the use of three colors isn't absolutely necessary. I do like the use of color, but it makes it glaringly obvious (to me) that the Midwest/Frontier map should also have distinguishing colors. If the decision is made to keep the Midwest/Frontier map in one color, I would show this map in only one color (two, technically) as well.
Regarding booking, if a flight can't be found when booking a flight and the "error" screen is presented, the "Back" button should work like the "Modify Search" link does. I would also add a "Modify Search" button next to the "Continue" button so that it can be more easily found. I had a difficult time finding the "Modify Search" link, and was hitting my browser's back button without success.