Longest hypercube path

Husk, 27 26 24 bytes

→foΛεẊδṁ≠ÖLm↓≠⁰←ġ→PΠmṠe¬

Brute force, so very slow. Try it online!

Explanation

Husk reads naturally from right to left.

←ġ→PΠmṠe¬  Hypercube sequences ending in second input, say y=[1,1,0]
     mṠe¬  Pair each element with its negation: [[0,1],[0,1],[1,0]]
    Π      Cartesian product: [[0,0,1],[1,0,1],..,[1,1,0]]
   P       Permutations.
 ġ→        Group by last element
←          and take first group.
           The permutations are ordered so that those with last element y come first,
           so they are grouped together and returned here.

ÖLm↓≠⁰  Find first input.
  m     For each permutation,
   ↓≠⁰  drop all elements before the first input.
ÖL      Sort by length.

foΛεẊδṁ≠  Check path condition.
fo        Keep those lists that satisfy:
    Ẋ      For each adjacent pair (e.g. [0,1,0] and [1,1,0]),
      ṁ    take sum of
       ≠   absolute differences
     δ     of corresponding elements: 1+0+0 gives 1.
  Λε       Each value is at most 1.

→  Finally, return last element (which has greatest length).

Mathematica, 108 bytes

a=#~FromDigits~2+1&;Last@PadLeft[IntegerDigits[#-1,2]&/@FindPath[HypercubeGraph@Length@#,a@#,a@#2,∞,All]]&

Input:

[{0, 0, 0, 0}, {1, 1, 1, 1}]

Output:

{{0, 0, 0, 0}, {0, 0, 0, 1}, {0, 0, 1, 1}, {0, 0, 1, 0}, {0, 1, 1, 0},
 {0, 1, 0, 0}, {0, 1, 0, 1}, {1, 1, 0, 1}, {1, 0, 0, 1}, {1, 0, 0, 0},
 {1, 1, 0, 0}, {1, 1, 1, 0}, {1, 0, 1, 0}, {1, 0, 1, 1}, {1, 1, 1, 1}}

Mathematica, 175 bytes

Nice first question!

(m=#;n=#2;Last@SortBy[(S=Select)[S[Rest@Flatten[Permutations/@Subsets[Tuples[{0,1},(L=Length)@m]],1],First@#==m&&Last@#==n&],Union[EditDistance@@@Partition[#,2,1]]=={1}&],L])&   

Input

[{0, 0, 0}, {1, 1, 1}]