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As someone who has over 300 matches in ranked with AP Yi between season two and season three. I am happy to say that AP Master Yi is stronger then ever with the season three changes. So for those interested, here is my new item build for him.
1: Athene's Unholy Grail. This item allows you to stay in lane forever. And I mean forever. You also don't run out of mana during team fights because it gives you a percentage back each time you grab a kill. I've always had a problem with this, hence the reason I now add it as my first item.
2: Deathfire Grasp. This item is the new overpowered on any middle burst champion. Make sure you cast this on your target before you alpha strike.
3. Liandry's Torment / Deathcap. Now I am kind of torn on which item I want for a third item. After looking at the passive on LT, I personally will be getting this as a third item over Deathcap. Not only does it offer nice ability power, health, and magic penetration, the 5% burn of their percentage health is pretty beast. It even doubles if the enemy team has any kind of CC on them. Which means if you have an Amumu on your team. Oh god the damage.
4. Deathcap. Obviously.
5. Void Staff / Lichbane. Obviously if you want more magic penetration get Void Staff. Otherwise get Lichbane.
This is just my order in which I will build items. Other items that are good with Yi is Hourglass.