Bit late, but I wanted to share my opinion on this.

I faced this problem recently when I found a Java project with both libraries and they were used at the same time.

I think that org.json is easier to read and to use, for 2 main reasons (for my needs):

1. JsonObject is immutable. You can't add new key/value pairs to an already existing JsonObject (reference here: javax.json: Add new JsonNumber to existing JsonObject)

2. It takes a few lines to pretty print a JsonObject or JsonArray, while it only takes 1 line to do it with JSONObject or JSONArray. Example:

   CopyStringWriter sw = new StringWriter();
   Map<String, Object> properties = new HashMap<>();
   properties.put(JsonGenerator.PRETTY_PRINTING, true);
   
   JsonWriterFactory writerFactory = Json.createWriterFactory(properties);
   JsonWriter jsonWriter = writerFactory.createWriter(sw);
   
   jsonWriter.writeObject(jsonObject); //JsonObject created before
   jsonWriter.close();
   String prettyPrintedJSON = sw.toString();
   

That is the code I use to get an indented JSON to write to a file. And with org.json I only need jsonObject.toString(4).

Another difference is the constructors. You will need a JsonObjectBuilder to create a JSON with javax.json. One step more that can be avoided.

I'm sure there are more differences (not sure if it's possible to create a JsonObject from a String) but these are my thoughts.