He only has 2 abilities that directly benefit from AP and that is his alphastrike and meditate. His E and R don't benefit from AP AT ALL! Only reason AP yi is a considerable threat is if your teamfights are taking so long that he can throw multiple alphastrikes.
How to kill AP Yi:
1. He alphastrikes into the fight
2. Focus him (don't stun yet)
3. He starts meditating. CC him (pref stun)
4. Kill before stun wears off and he can ult and run off
Not really rocket science, although I'll admit his earlygame laning phase is OP as hell without your jungler ganking him right after an alpha strike.