A few things.
I can respect that someone wouldn't enjoy the slow pace, structure or tone conveyed by the form employed. It's not for everyone and it's something you must become accustomed to or be predisposed to. However, while some may find it distracting and confusing, others may see it as the near perfection of an art form, as I do.
Critiques regarding the weirdness or saying that it cannot be understood and that it is not intended to be understood are incorrect. I believe I correctly understand it. In general, it's about a family (especially a son, mother and father) and their place in the cosmos (which is not insignificant) and in relation to God, as well as a Christian understanding of nature vs. grace. I think that every frame intentionally supports these purposes, using additional material (light, sin, death, etc.) for clarity. A background with these subjects can help. I've seen it several times, but did not need to to form a basic understanding of what is occurring.
I cared for the characters immediately, I saw myself in them.
Feces on a table is not valid. The Tree of Life uses a form and means of expression that are valid, without pretension. And a director's cut does not officially exist and probably never will. If it ever does, it will be because footage was shot that would further aid the vision of the director.