What do you think?
As far as I remember, Navi only tells you to go to the desert after you've beaten the Shadow Temple. Also, the Nocturne of Shadow cutscene in Kakariko starts after you've beaten the Forest, Fire, and Water Temples. In this cutscene, evil escapes from the well and goes to the Shadow Temple. You then learn the Nocturne of Shadow immediately after. So the game is basically pushing you to beat Shadow immediately after getting the Lens of Truth from the well. Then after you beat Shadow, Navi tells you to go to the desert (correct me if I'm wrong). Also, Nintendo's official walkthrough of the game tells you to do Spirit last:
http://www.zelda.com/ocarina/walkthru.htmlSo I'm a "Spirit is last" guy.
The arguments that the "Shadow is last" guys have is:
1. The Shadow Medallion is after Spirit Medallion on the quest screen and file select screen.
2. After beating Shadow, Impa says "Soon you will meet Zelda face to face" (although soon is a pretty broad term, which could easily be refering to "after the next temple").
3. You need to meet more game requirements to enter Shadow than you do in order to enter Spirit.
4. Ice Arrows are effective on Bongo Bongo's hands (although they also work on Gerudo's, which implies leftover programming).
5. Blinking dots of map tell you to go to the desert after beating water.