Okay, a while back I bought and played the Naruto game for the 360. I'm probably the only non-fanboy who bought it, certainly the only one who beat it, but I think it may be the absolute best "design teaching" game I've ever seen. Since it's usually available in discount bins, I would suggest you pick it up and play it if you have some time.
This is not an endorsement of the game per se, since it is unplayably bad at parts and extraordinarily dull at others. But it has the clearest good and bad points of any game I've ever played. There are no mysteries behind the design, no muddy parts, it's very clear what the pressures on them were, why they chose to do X or Y, and what the final result is in terms of gameplay and audience approval.
I'm going to give the example I like best: the Leaf Ninja City. You spend a lot of time in the city, although all of the plot and interesting stuff actually happens outside the city. The city is just there for you to run around in.
And it is hands down the best multi-tier revisitable level design I have ever seen.
In the beginning, you run around the city in the streets. You get some coins, painstakingly scramble up onto a few roofs, find a few stores, and get a few people to hate you slightly less. Of special note is that the city is extremely immersive in its way: it's quite pretty and packed chock-full of people who will call out to you as you go by. It also fits the IP well, as Naruto is widely disliked in the city at game start (people will call out rather nasty things), but as you do little side quests they come to like you.
It's all well and good, but not particularly awesome.
Then you start getting additional ninja powers. I don't remember what order you get them in, but you gain double-jump, sprint, and wall climb. The city never changes, but you flawlessly - utterly flawlessly - find that it is far more interesting to navigate. You aren't finding new "areas", like in Metroid: you're literally just a bit higher up than you were before, running along a different path.
If you want an example of how to design a "home" level that will change over the course of the game while always being the same, this is probably the best example you'll ever find. By the end of the game, you and your city have grown very close. It's actually quite good.
Of course, there are still a lot of weaknesses, probably due to the target audience. The city is full of random side quests, but they are all particularly boring and repetitive. There are very few places that make you stop and say, "wow!", which is a requirement for any exploration-based game. Oh, and the rest of the game is really irritating.
But if you're looking for a game to learn from, this is probably the right choice. In terms of revisitable multi-tier levels, it even beats out Crackdown, which has always been one of my major examples.