It seems that the Western language of Buddhism is stuck in some fundamental ways in a psychological vocabulary long extinct. I easily read 1 to 5 bits of Buddhist ephemera a day (blog posts, Facebook comments, etc...) that use the word 'ego' as if it means something.
I think that ultimately Buddha, and the many of the great leaders of Zen thought were striving to understand the human 'self'. The self-experience. How the human perception of the world gives rise to suffering. How I interact with my surroundings, how my person was informed by past events, that gives rise to my 'now.' Buddhism is a science, but importantly, a practical science, not a science of wild un-experienceable theories. I love the phrase 'natural philosophy' so I'll marry it with Buddhism. Buddhism, and I think most specifically Zen, is the attempt to really probe human experience as a practical reality, which must admit the role of mind. Zen strives to unravel mind, to step outside mind. To SEE mind.
Therefore Zen does not look well on theories alone. Zen trips up theories in subtle and important ways. "Pain is only the mind a work, I have transcended it" -- until you stub your toe and cry "ouch". You have transcended nothing, Zen teaches.
Zen-speak is very stuck on ego. But serious Zen practitioners (or perhaps l should be more generous and simply say, practitioners who are striving for the truth in the manner I expound above), should be very careful of the idea-set that has "ego" at its center. Zen is a science, and must move forward with new understandings in how mind works and how "self" is experienced in the body.
I think the ancients knew well how "things worked" in the human experience. I think the ancients did their best to express what they saw and knew. It think many translations and subsequent teachers using English have completely mis-colored Zen with the idea of Ego.
Ego was largely invented by Freud and is now largely discredited. It no long has meaning. It was a theory set of how the mind works that is no longer held by most modern technical analysts of the human condition. "Ego" was just a fantasy of Freud that appealed as religion to the tribal lust of a generation. It was not based on scientific method.
Quoting from io9.com "Why Freud Still Matters, When He Was Wrong About Almost Everything" (Emphasis added)