I haven't figured out how the code share pricing works. I checked some various city pairs and priced them out to the point of purchase on both websites, using exactly the same flights on the same dates.

10/1 to 10/7 round trip for idential flights

Both fares identical:

RDU $224.50
GSO $194.00
PVD $218.50
ROC $198.50
PBI $267.50

Midwest more expensive than nwa.com.

FLL
$204.50 total booked on nwa.com
$300.00 total booked on midwestairlines.com -- $95.50 more

AVL
$228.50 total booked on nwa.com
$338.50 total booked on midwestairlines.com -- $110.00 more

PDX
$279.50 total booked on nwa.com
$288.50 total booked on midwestairlines.com -- $9.00 more

Midwest less expensive than nwa.com

RSW
$334.50 on nwa.com
$271.50 on midwestairlines.com -- $63.00 less

ABQ
$385.00 on nwa.com
$363.00 on midwestairlines.com -- $22.00 less

The fare differences...when they exist...don't seem to be any set amount. Two examples were cheaper on midwest than on nwa, which seems particularly odd.

Not that it makes this any better, but in pricing trips over the past few years I've seen a lot of strangeness between code share partners DL/NW and UA/US, at least on sites like orbitz and travelocity, and the online booking tool at work (horizon). Strangeness where the very same nonstop segment was $200 on one airline and $600 on the other, and not always the "true" airline being cheaper.