Much more conservative approach to disk space management – each MyISAM table is stored in a separate file, which could be compressed then with myisamchk if needed.
With InnoDB the tables are stored in tablespace and not much further optimization is possible. All data except for TEXT and BLOB can occupy 8,000 bytes at most. No full text indexing is available for InnoDB. The COUNT(*)s execute slower than in MyISAM due to tablespace complexity.