I paddle the Minnesota at least once a year.  
The only sections I've paddled are between Belle Plain and the Mississippi.
There are some strange dangers on the Minnesota.  
In high water there are a lot of submerged logs and trees traveling in their own direction that'll make you tighten up your pfd in a hurry. Usually not that big of a deal. I just pay a lot of attention of what's behind me.
Some sandbars can be a little hairy to get out on. The eddies and under lying currents can grab a boat below the water line making it a little tough to get in and out. Making good entrance and exit decisions important.  
Water quality is also some of the lowest in the state. It isn't uncommon to see mystery barrels on the shore line. Also It drains a huge stretch of farmland so there's a lot fertilizers and soil errosion contributing to clarity. IMHO the Minnesota looks as good or better than most comparable rivers in Iowa but stands out as polluted river in MN.
All draw backs aside it is a beautiful valley of tall cottonwoods and sugar maples to paddle with a quick flow that'll keep you on your toes all the while containing some of the best Catfish fishing in the state. My personal biggest fish ever was a Flathead in Shakopee at 39lbs. Also my biggest and only sheepshead at 5lbs.
I would say that the Minnesota is a great MOVING water paddle. A persons level of comfort, and experience in moving water is what will make the Minnesota a good paddle.

Oh ya. There's a couple of these known to wandering around down there too. [smiley=thumbdown.gif]
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Hope this helps.  

SW