The table should be innodb on installation as that is our convention - it also allows you to separate the stats table into its own data file (which is handy because it can get rather large).
Having its own data file might improve write performance, if that file is on a separate physical medium. Have you measured the number of transactions? Sounds like it might be rather large.
As for the insert - it could most likely be made more efficient in code - we issue individual inserts at the moment, in a transaction. These could be batched outside of a transaction.