Welcome to the FAQ website covering document topics in Canada.
My wife and I are married and living in Japan, but I will have to return to Canada 05/16. Would it be more advisable for her to apply for permanent residence from outside Canada (right to appeal/shorter processing time), or from Inland (as we could live together indefinitely while waiting).
The biggest difference is in processing time, but you seem to know that already. Frankly, it’s up to you both, but if you want to live together sooner, inland seems to be the better choice.