To answer your question, the answer is there really is no definitive reason to avoid a more direct Brainerd to say Haywood, WI route other than places/things you may want to see in Minneapolis/St. Paul area. If you create a direct route, I would definitely check out Minnesota's and Wisconsin's official bike maps to avoid getting on high traffic roads though.
IIRC, the North Lakes Route and Lake Erie Connector were added after the NT was established. I am guessing that the route designers probably wanted a junction with a major transportation hub so Minneapolis was it. Remember, in the scope of a major cross country route (Washington State to Maine), a route is going to zig zag occasionally. A mid-route zig zag may very well have to do with traffic counts and/or lack of decent roads, lack of services (food, lodging, etc.), and/or significant points of interest.
Since I assume you are still looking to ride between Winnigpeg and Ann Arbor, you might consider a different route. I love riding in Wisconsin, especially the Driftless area (hilly but bucolic).
A route I would personally consider is to ride down to Fargo (see above in this thread for routes), then take the Northern Tier to LaCrosse, WI, where I would pick up the various rail trails or even some different routes (see below) that take you all the way to Milwaukee. Then you would take the ferry to Muskegon and from there, the various rail trails to St Johns, MI, before creating my own route to Ann Arbor. The big negative is you miss Mackinac Island.
Here is a collection of maps for reference:
https://ridewithgps.com/collections/54989?privacy_code=3XmzOFv1x698fxdN . Note this collection (I call it the Heartland Express) is not completed yet so the maps do not show campgroudns, grocery stores, hotels, etc. However, I have ridden all of it (some slight deviations here and there) and enjoyed it.
As a side note, if you have suggestions for a route from St. Johns to Ann Arbor and/or Algonac, I would be very interested.
Tailwinds, John