He uses poor OpenGL practices, and sees poor performance as a result. He also designed the entire product in a way that makes it cumbersome to mod, without a consistent interface or a logical way for mods to work together. Modding Minecraft as a whole is one big hack.
I'm more familiar with the networking side of things. The Minecraft networking protocol is a mess. There are 9 or 10 different ways to encode a vector in the protocol. He made up "Named Binary Tags", a dictionary serialization format, which could have better been served with existing tech. He frequently misuses signedness in the protocol. He made up another obtuse dictionary format for describing entity metadata. He screwed up backwards compatibility for the only thing that needed to be backwards compatible - three times. His colleagues later screwed things up even more.