-- in table2 but not in table1:
SELECT r.id
FROM table2 AS r
LEFT JOIN table1 AS l
  ON r.id = l.id
WHERE
       r.system = ?
   and l.id IS NULL
   and r.id IS NOT NULL

-- in table1 but not in table2:
SELECT l.id
FROM table2 AS l
LEFT JOIN table1 AS r
  ON l.id = r.id
WHERE
       l.system = ?
   and l.id IS NOT NULL
   and r.id IS NULL
SQL