If it's the application's responsibility to bundle the schema in Avro, then one difference is that Ion takes responsibility for embedding schema information along with each structure and field. Ion is also capable of representing data where there is no schema (analogy: a complex document like an HTML5 page), or working efficiently with large structures without deserializing everything even if the application needs data in just one field.
Another platform in contrast with Ion is Apache Parquet [1]. Parquet's support for columnar data means that it can serialize and compress table-like data extremely efficiently (it serializes all values in one column, followed by the next, until the end of a chunk -- enabling efficient compression as well as efficient column scans). Ion by comparison would serialize each row and field within it in a self-describing way (even though that information is redundant, in this particular case, since all rows are the same). Great flexibility and high fidelity at the expense of efficiency.