I too have wondered about Voyageurs and Isle Royale. I have always found real difficulty getting info. about how to get to them on the internet. I am a big planner. I know there is a ferry, but I can't ever seem to find a schedule. Obviously people go there, but search me how they do it.
What I can help you with is the rest of the north shore. We LOVE the Minnesota North Shore along Lake Superior. Not only is the lake part awesome, but there are tons of great rivers to hike along as well. You can hike all day and see waterfall after waterfall after waterfall. It's awesome! Here are some suggestions for parks:
Here's a map so you can find them on the upper right side: http://www.dnr.state.mn.us/state_parks/map.html
1. Gooseberry Falls: I consider this the "Disneyland" of the North Shore Parks because it's always crawling with tourists. Why? It is free to park there even in their lots. It is also the closest park to Duluth. I don't like that it is always crawling with people, but it's free, so why not stop.
2. Tettegouche and Temperance River - Both of these parks are awesome! Great hiking, great rivers and waterfalls. http://www.dnr.state.mn.us/state_parks/tettegouche/index.html
3. Judge C.R. Magney - This park is beautiful as well, but what it's really know for is "Devil's Kettle." It's a rock formation in the river that swirls around and goes down a hole. No one knows where it goes. It's pretty cool and you can hike out and look right in it. However, if it's a dry year prepare to be disappointed. We went there last summer and the river was too low for there to be anything exciting going on there. Here's a pretty good picture. http://www.gowaterfalling.com/waterfalls/devilskettle.shtml
Also, one of my favorite places that not many know about is Beaver Bay. It's a tiny town between Two Harbors and Grand Marais. When you start to leave Beaver Bay you cross a bridge. You can park in a lot right before you cross the bridge. Under that bridge is a great river. If you you cross the bridge on foot and head down to the lake, you will see a sign that says, "Private Property - Please Enjoy and leave it as you found it." How great is that? On the lake side you can sit all afternoon combing through the rocks and picking out tiny agates. The river that feeds into the lake is great fun to hike up. There is a trail alongside it, but my husband and I have spent many a beautiful sunny day walking up in the river - climbing rocks etc. There are tons of awesome little waterfalls. Pack and lunch and bring some good shoes for tromping in the water.
Honestly, we've never been disappointed in any of the places we've gone on the North Shore.
If you like art, Grand Marais has a great artist community. The Angry Trout is a great restaurant where everything is local, sustainable, and made by hand (including tables, chairs, napkins...) oh, and the food is great! The World's Best Donut shop is pretty swell too. Good thing we're heading up to the North Shore in a couple of weeks. Writing all this is really making me miss it!
I could go on and on about restaurants, shops, great people. So, even if you don't make it to Voyageurs it's worth a trip to MN's North Shore!