W/ the exception of E. CO, I've been all over NE, ND, SD, MN, and MI, some by bike and a lot by car. So much of your choice depends on time and preference. For me, about anything rural works as I enjoy cruising through the small towns, seeing the farmland, etc. If you want a bit more adventurous, I'd head N toward Rapid City, through the NE panhandle....long hills, often straight roads, but the traffic count goes way down....along with services. DON'T go clear into northern ND as they're in an oil boom...no motels, high prices, bad roads. We took a good road into Sturgis from the E a few years ago, Hwy 34. It has a big S jog so you might want to head N at Howes.
I know I'm old-fashioned, but I really love having a paper map, visualizing what I'm shooting for, what part of the state I want to see, etc... and I get a better feel for how major a road I'm going to use. If you have time and sun....it's fun to just meander in the general direction you want to go, but in SD that can burn up a lot of time and you might hit a town with no place to stay....esp. in the north.
Anyway, that would be my choice....N to the Black Hills/Badlands, edge N across SD and MN aiming, ultimately for Duluth, and, in agreement with SCBonne, ride around Superior on the N side, and on to wherever in MI you're heading.
If you're more the farmer type...follow the NE/KS border (got now idea which roads), take Hwy. 2 (the only road across the state with hills) all the way across IA (I grew up about halfway across) to the Mississippi, follow it N (might be high traffic, but there are some access roads that can be quite scenic) clear to WI, and angle NE across the state to the UP. I rode bicycle in SW WI quite a bit and there are a lot of paved county roads that meander quite nicely. Stop in Green Bay and check out Packer stadium....I hate them, but love the ambiance.
Any questions just let me know....and have fun planning.