A little Chicago in Rochester MN
Its tough, chicago is such a great food city and rochester is home to a lot of chain restaurants. Do a search on here for the best recs, but its kinda thin soup. One must try is the harborview in Pepin WI. Great date place and a pretty drive especially in Summer. For greasy spoon try cheap charlies. Good luck
I lived in Rochester for 2 years after having moved from LA and feel your pain.
Harborview - definitely the best in ALL of your area, but a bit of a drive for a nice weekday dinner and they don't take reservations.
Redwood Room - overrated and just-OK, but the ambience and basement location is cozy on a cold winters night.
The Good Food Store - has a deli in the back that has awesome, AWESOME vegan food, even though I'm not even a vegan.
Canadian Honker - though very average in most of their foods, their beef barley soup is pretty good.
You'll hear about all the other places that those in Rochester will highly recommend and tout as "excellent", but don't believe the hype - they're just average in any other city. If you're a real foodie, you'll find yourself driving to the TC every weekend for real, good food: Origami, Lucia, Broder's, Chiang Mai Thai.
In regards to The Harbor View http://www.harborviewpepin.com/
They are closed for the season now and will reopen in march. They are not open all week long, check their website for hours. It is an hour drive from Rochester to Pepin. Best way to go is through Plainview and then up hwy 61 to Wabasha.
We have another interesting restaurant in Pepin called the Garden Pub and Grill. They were more of a regular grill/pub the first year they were open, they went more gourmet this last year. If you want to try something a little further away I hear Nortons is fantastic which is up the river from us in between Bay City, WI and Hager City, WI. I have not eaten there personally, but I hear really great things from coworkers. A little higher end in prices like the harbor view would be, but I hear it is quite worth it.
There is also a great restaurant in Red Wing, MN called Oar'dourve. They have a nice twist on dinner with a boating theme in the restaurant. A martini menu and interesteing appetizers and great meals like butternut squash ravioli and a chicken sandwich marinated in raspberry vinegrette.
The another place that is worth trying around our area, is The Anderson House in Wabasha.
They have a wide selection of food and it is quite reasonable. The fish dinner is usually what I have. Everything that comes out of the kitchen all looks great. They do lunch and dinner, and have a great breakfast buffet also. It is a hotel also if you wanted to stay in the area.