The biggest advantage of SparkR is the ability to run on Spark arbitrary user-defined functions written in R:
https://spark.apache.org/docs/2.0.1/sparkr.html#applying-user-defined-function
Since sparklyr translates R to SQL, you can only use very small set of functions in mutate
statements:
http://spark.rstudio.com/dplyr.html#sql_translation
That deficiency is somewhat alleviated by Extensions (http://spark.rstudio.com/extensions.html#wrapper_functions).
Other than that, sparklyr is a winner (in my opinion). Aside from the obvious advantage of using familiar dplyr
functions, sparklyr has much more comprehensive API for MLlib (http://spark.rstudio.com/mllib.html) and the Extensions mentioned above.