Considerable size difference between mysql versions
I suggest looking at the 5.6/5.7 release notes to see what changed from 5.5.

ib_logfile file size are because the innodb_log_file_size changed from the outrageously small value of 5M to something that actually performs when people update any modest amount of data.

The ibdata1 increase in size might be a result of utf8_mb4 being the default.

System tables support more features and have some bigger fields.

Overall, its not that much. Are you really running on an embedded processor?