I find the use of the former Submarine attraction's space at MK to be a positive "trade-up" to the New Fantasyland.
Despite my avatar, I agree with the premise, though I think the time lag between the closure of 20K and the opening of New Fantasyland makes it difficult to draw a straight line between the two. Overall, New Fantasyland was a trade up over the lagoon. But I do miss Toontown. Well...maybe not personally. But the concept and execution of Toontown and the character meet and greets that it provided were brilliantly executed.
Many other examples have already been cited. Such as Food Rocks--->Soarin'. And Snow White---->Mine Train. So here are a couple more.
I thought I would miss the Wonders of Life Pavilion, but I love what they put in its place.
I thought I would miss the Odyssey Restaurant , but I love what they put in its place.
I thought I would miss the second floor of the Imagination Pavilion, but I love what they put in its place.
I thought I would miss the Tomorrowland Noodle Station, but I love what they put in its place.
I thought I would miss the Swan Boats, but I love what they put in its place.
Removing tongue from cheek now.