Per the website, there are daily flights (United) to the Houghton airport (eight miles S of town). They don't mention shuttle services, but I am pretty sure they exist. In some way Yosemite is probably ideal, but I think Isle Royale is a prime example of a really neat place that is definitely uncrowded, unlike some parts of Yosemite. And, of course, while you are in that neck of the woods, you can drop by Pipestone National Monument, another hidden gem. No public transportation there, but it is accessible by bicycle - that is how I got there.

Actually there are scads more trails at Yosemite that at Isle Royale, and some of the more isolated Yosemite trails are probably just about as unfrequented.