Array of arrays = No serialization?

Just do an array of objects with an array in them, and Unity will serialize that and be able to show it in the editor just fine:

public class ThingWithArraysOfArrays : ScriptableObject 
{
    [System.Serializable]
    public class ThingWithArrays
    {
        public int[] array;
    }
    public ThingWithArrays[] array;
}

that will solve your serialization problem at the cost of accessing the nested array like: container.array[x].array[y] instead of container.array[x][y], but if that's a problem, you could try adding an overload of the [] operator to the ThingWithArrays like this:

public int this[int i]
{
    get
    {
        return array[i];
    }
    set
    {
        array[i] = value;
    }
}

... and if you are using javascript instead of C#, well sorry.

Usually there are ways to get around the limitations of Unity's serialization system. One option in your case might be to create a serializable custom class that has an array as a member, and then create an array whose element type is that class (I think this would work, but I'd have to try it to be sure). If you're just wanting a (square) 2-d array, another option would be to store the data as a 1-d array and provide accessors that support 2-d indexing.

If you want a 2D array, then you should be able to implement this into your project.

I used a hashtable of hashtables to save the objects in my project, using the propertylist serializer on the wiki.

for it to work though I had to have an array that stored the name of each sub hash table, that way I would know what to iterate through.