Word transformation function
If true, true. If false, false.

Your code is filled with situations like this:

if someCondition:
    variable = True
else:
    variable = False


You can replace all those occurrences with a simple assignment:

variable = someCondition


If, and if not

Additionally, there's no need to add == True in a comparison. The Python way of x == False is to do not x

Conditional ternary operator

if wordy11:
    wordy = "sametrue"
else:
    wordy = "samefalse"


Can be written as:

wordy = "sametrue" if wordy11 else "samefalse"


Variable names

What on earth is wordy? What type is it? It seems to be one variable used for all kinds of things. I'd recommend making these separate variables and using more descriptive variable names.

Result

This will clean up your code a bit at least, to this point:

"""Docstring"""
import words


def nicer_englishify_word(word):
    """Docstring"""
    wordx = word.lower()
    wordy = ""

    if wordx.endswith('moo'):
        wordy1 = wordx[-3] + wordx[:-3]
        wordy2 = wordx[:-3]
        wordy11 = wordy1 in words.get_word_list()
        wordy22 = wordy2 in words.get_word_list()
        if wordy11 == wordy22:
            wordy = "sametrue" if wordy11 else "samefalse"
        else:
            if not wordy22:
                wordy = "[" + wordx[-3] + wordx[:-3] + "]"    
            else:
                wordy = "[" + wordx[:-3] + "]"
        wordy = wordx[-3] + wordx[:-3] + " or " + wordx[:-3]
        wordy = "&lt;" + wordy + "&gt;" if wordy == "sametrue" else "(" + wordy + ")"
    else:
        wordy = wordx[-3] + wordx[:-3]
    return wordy