org.apache.spark.mllib is the first of the two Spark APIs while org.apache.spark.ml is the new API.
However, the spark.ml is considered as the recommended package because with DataFrames the API is more versatile and flexible. But users will keep supporting spark.mllib along with the development of spark.ml. Users should be comfortable using spark.mllib features as for existing algorithms not all of the functionality has been ported over to the new Spark ML API. But it is expected to have more features in the coming time.
In Spark 2.0, the RDD-based APIs in the spark.mllib package have entered maintenance mode. The primary Machine Learning API for Spark has now changed to the DataFrame-based API in the spark.ml package. Now mllib is slowly getting deprecated(this already happened in case of linear regression) and most probably will be removed in the next major release.