I\'m unsure about whether to use a mutable struct or a mutable class. My program stores an array with a lot of objects. I\'ve noticed that using a class doubles the amount of me
First off, if you really want to save memory then don't be using a struct or a class.
byte[,,] blockTypes = new byte[16, 256, 16];
BlockMetaData[,,] blockMetadata = new BlockMetaData[16, 256, 16];
You want to tightly pack similar things together in memory. You never want to put a byte next to a reference in a struct if you can possibly avoid it; such a struct will waste three to seven bytes automatically. References have to be word-aligned in .NET.
Second, I'm assuming that you're building a voxel system here. There might be a better way to represent the voxels than a 3-d array, depending on their distribution. If you are going to be making a truly enormous number of these things then store them in an immutable octree. By using the persistence properties of the immutable octree you can make cubic structures with quadrillions of voxels in them so long as the universe you are representing is "clumpy". That is, there are large regions of similarity throughout the world. You trade somewhat larger O(lg n) time for accessing and changing elements, but you get to have way, way more elements to work with.
Third, "ID" is a really bad way to represent the concept of "type". When I see "ID" I assume that the number uniquely identifies the element, not describes it. Consider changing the name to something less confusing.
Fourth, how many of the elements have metadata? You can probably do far better than an array of references if the number of elements with metadata is small compared to the total number of elements. Consider a sparse array approach; sparse arrays are much more space efficient.