We found a large percentage of transaction time is spent in questionnaire/view.php and questionnaire/complete.php due to this query:

SELECT * FROM mdl_questionnaire_quest_choice WHERE question_id = ? ORDER BY id ASC

There is no index on question_id. We added such an index and experienced gains in performance.

alter table mdl_questionnaire_quest_choice add index mdl_quest_choice_quesidx (question_id);