As for MKE-MCI-LAX trouble, I've seen those via-MCI west coast connections periodically missing on days when clearly they are not sold out. (Sold out on one leg or the other is always a possibility, of course.) Not sure what's up with that, but obviously it's something they should remedy. You got the flights you wanted because you knew they were supposed to be there and called, but other people will instead choose one of the via-Denver connections or book elsewhere.

The old Midwest site was plagued with that kind of problem, especially when the NW code sharing flights were there, because it only show a certain number of flights and chose the cheapest ones. So if you were looking for MKE-SEA the actual YX flights were often croweded out by a variety of MKE-MSP-SEA flights (including MKE-MSP on either YX or NW) and the MKE-SEA nonstop or via-MCI flight didn't show.

There doesn't appear as clear or obvious a reason why sometimes flights like SEA-MCI-MKE don't show among the SEA-DEN-MKE options. At least not yet. But hopefully they are more successful than Midwest was at correcting missing flights. The only thing which really ended the YX problem was when they stopped code-sharing with NW/DL and all those connecting options were gone.