My favorite river route is from the Kettle River put in at Hwy 48 just east of Hinckley to the St Croix River landing at Hwy 70.  A nice mix of scenery, still water and canoeable rapids.

I've been on the Snake, Kettle, St Criox (from St Croix Sate Park to Taylors Falls), Cloquet, St Louis, Rum, Mississippi and Vermillion.  Depending on your personal preference for scenery, fishing, crowds, whitewater, etc. each has its own flavor.

CC (Canoe Country) Tripper

more specifically...ive narrowed it down.   mid september.   either the upper miss (as far as anoka)  or the upper st.croix. 

we want to do a 3-4 night trip.  first river trip ever!  so....i need some suggestions.

good fishing is semi-importment......semi.

i have "paddling minnesota"  but would also like some input from here.

thank you all       Jan

Well I have only been on the Mississippi between St. Cloud and Elk River.  The fishing is really really great but there are houses everywhere- not very scenic.  So if you want fishing go to the Mississippi but if you want wilderness go to the St. Croix because it has good fishing and few houses.   

I've been down most of the "designated canole routes". The St. Croix is always fun for smallmouth. The upper can get really shallow this time year especially up by the Namakogen.
The Kettle is always a good time unless it's really low. State record for catfish or sturgeon came out of there. Forgot which.
The Root is neat trip. It's southern MN. It flows east to the Mississippi. Pretty river runs through a deap canyon for a while. Amazing amount of Barn Swallows. Some swift water but barely worth worring about. Allot of Turkey Vultures. Really good trout fishing. Most of the campsites are maintained. Been a couple of years since I've been there. The last time I had dead cow in the campsite. Of course it wasn't until we had everthing set up before we were wondering what stunk so bad.
The upper Miss. is beautiful, nice fishing. Too many dams. It always felt a little artificial.
The Little Fork was a really good time. GREAT STURGEON FISHING, if that were legal. We caught several by accident. The largest was 41lbs. Also allot of Whitefish, Snot-rockets, and even a couple Wallys. Hardly any houses. Really fun rapids. Pretty waterfalls. Some great campsites. The bad part is that in low water the banks are really steep making it really hard to get out of the boat. Also the clay is so thick and sticky I still have some on my tent today. Probably the most remote river trip I've ever been on in MN.
The Rum is fun. Easily accesible.
The Cannon is also a really nice paddle. Pretty consistant water level. Really fun trip if started on the Straight river in Fairbault and finish at the bridge on 61 just north of Red Wing, before the Missisippi river. Really pretty trip. Also great shopping or restarants. A person could even spend the night in a hotel each night if they wanted.

SW

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.
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Hope this helps. 

SW