Here is a contribution that treats the full symmetry group of the hypercube, not just rigid motions. This group can be obtained by labelling the vertices of the cube with the $2^n$ bit strings of length $n$ where adjacency is equivalent to having one bit different between two vertices. Then we obtain the full vertex permutation group of the hypercube by combining bit flips with bit position permutations e.g. combine a particular bit flip with a particular permutation of the bits and the result is an automorphism. Once we have these permutations we can use them to compute the induced permutation group on the two-faces.
This gives the following cycle indices for the face permutation groups containing rotations and reflections: for $n=2,$ $$a_{{1}},$$
for $n=3$,
$$1/48\,{a_{{1}}}^{6}+3/16\,{a_{{2}}}^{2}{a_{{1}}}^{2}+1/6\,{a_{{3}}}^{2}+1/16\,{a_{{1
}}}^{4}a_{{2}}\\+{\frac {7}{48}}\,{a_{{2}}}^{3}+1/8\,{a_{{1}}}^{2}a_{{4}}+1/6\,a_{{6}}
+1/8\,a_{{4}}a_{{2}},$$
for $n=4$,
$${\frac {1}{384}}\,{a_{{1}}}^{24}+1/32\,{a_{{1}}}^{6}{a_{{2}}}^{9}+1/12\,{a_{{3}}}^{8
}+{\frac {3}{64}}\,{a_{{1}}}^{4}{a_{{2}}}^{10}+{\frac {7}{32}}\,{a_{{4}}}^{5}{a_{{2}
}}^{2}+{\frac {1}{96}}\,{a_{{1}}}^{12}{a_{{2}}}^{6}\\+{\frac {3}{32}}\,{a_{{1}}}^{2}{a
_{{2}}}^{11}+1/12\,{a_{{3}}}^{4}{a_{{6}}}^{2}+1/32\,{a_{{1}}}^{4}{a_{{4}}}^{5}\\+1/16
\,{a_{{1}}}^{2}a_{{2}}{a_{{4}}}^{5}+1/6\,{a_{{6}}}^{4}+1/8\,{a_{{8}}}^{3}+1/32\,{a_{
{4}}}^{6}+{\frac {5}{384}}\,{a_{{2}}}^{12},$$
and for $n=5$,
$${\frac {1}{3840}}\,{a_{{1}}}^{80}+{\frac {1}{192}}\,{a_{{1}}}^{20}{a_{{2}}}^{30}+1/
48\,{a_{{1}}}^{2}{a_{{3}}}^{26}+{\frac {13}{384}}\,{a_{{2}}}^{36}{a_{{1}}}^{8}\\+{
\frac {37}{192}}\,{a_{{4}}}^{18}{a_{{2}}}^{4}+1/24\,{a_{{1}}}^{2}{a_{{3}}}^{6}{a_{{6
}}}^{10}+1/10\,{a_{{5}}}^{16}+{\frac {1}{768}}\,{a_{{1}}}^{32}{a_{{2}}}^{24}+1/24\,{
a_{{1}}}^{2}{a_{{3}}}^{10}{a_{{6}}}^{8}\\+1/40\,{a_{{2}}}^{40}+{\frac {1}{192}}\,{a_{{
1}}}^{8}{a_{{4}}}^{18}+1/32\,{a_{{1}}}^{4}{a_{{2}}}^{2}{a_{{4}}}^{18}+1/24\,{a_{{1}}
}^{2}{a_{{3}}}^{2}{a_{{12}}}^{6}\\+1/8\,{a_{{6}}}^{13}a_{{2}}+1/8\,{a_{{8}}}^{10}+1/10
\,{a_{{10}}}^{8}+{\frac {1}{64}}\,{a_{{1}}}^{4}{a_{{2}}}^{38}\\+1/48\,{a_{{1}}}^{2}{a_
{{3}}}^{2}{a_{{6}}}^{12}+1/32\,{a_{{4}}}^{20}+1/24\,{a_{{12}}}^{6}a_{{6}}a_{{2}} .$$
These directly produce the following formulas for the number of colorings with at most $N$ colors. For $n=2$, we get $$N.$$ For $n=3$ we get
$$1/48\,{N}^{6}+1/16\,{N}^{5}+3/16\,{N}^{4}+{\frac {13}{48}}\,{N}^{3}+{\frac {7}{24}}
\,{N}^{2}+1/6\,N, $$
for $n=4$ we get
$${\frac {1}{384}}\,{N}^{24}+{\frac {1}{96}}\,{N}^{18}+1/32\,{N}^{15}+{\frac {3}{64}}
\,{N}^{14}+{\frac {3}{32}}\,{N}^{13}+{\frac {5}{384}}\,{N}^{12}+1/32\,{N}^{9}+{
\frac {7}{48}}\,{N}^{8}\\+{\frac {7}{32}}\,{N}^{7}+{\frac {11}{96}}\,{N}^{6}+1/6\,{N}^
{4}+1/8\,{N}^{3},$$
and for $n=5$ we have
$${\frac {1}{3840}}\,{N}^{80}+{\frac {1}{768}}\,{N}^{56}+{\frac {1}{192}}\,{N}^{50}+{
\frac {13}{384}}\,{N}^{44}+{\frac {1}{64}}\,{N}^{42}+1/40\,{N}^{40}+1/48\,{N}^{28}+{
\frac {1}{192}}\,{N}^{26}+1/32\,{N}^{24}+{\frac {37}{192}}\,{N}^{22}+{\frac {7}{96}}
\,{N}^{20}+1/24\,{N}^{18}+{\frac {29}{240}}\,{N}^{16}+1/8\,{N}^{14}+1/6\,{N}^{10}+{
\frac {17}{120}}\,{N}^{8} .$$
Note that the case for $n=3$ is OEIS A198833.
These cycle indices were computed with the following Maple program.
with(combinat, permute);
with(combinat, choose);
pet_autom2cycles :=
proc(src, aut)
local numa, numsubs;
local marks, pos, cycs, cpos, clen;
numsubs := [seq(src[k]=k, k=1..nops(src))];
numa := subs(numsubs, aut);
marks := [seq(true, pos=1..nops(aut))];
cycs := []; pos := 1;
while pos <= nops(aut) do
if marks[pos] then
clen := 0; cpos := pos;
while marks[cpos] do
marks[cpos] := false;
cpos := numa[cpos];
clen := clen+1;
od;
cycs := [op(cycs), clen];
fi;
pos := pos+1;
od;
return mul(a[cycs[k]], k=1..nops(cycs));
end;
hypercube_face_cind :=
proc(dim)
option remember;
local verts, v1, v2, faces, f, ff, fv, k, m, b,
d2, pos, fpos, perm, fperm, act, s;
if dim=1 then return FAIL fi;
verts := [];
for k from 2^dim to 2^(dim+1)-1 do
b := convert(k, base, 2);
verts := [op(verts), [seq(b[m], m=1..dim)]];
od;
faces := [];
for d2 in choose(dim, 2) do
for k from 2^(dim-2) to 2^(dim-1)-1 do
b := convert(k, base, 2);
f := [];
for ff in [[0,0], [0,1], [1,0], [1,1]] do
fv := [seq(-1, pos=1..dim)];
fv[d2[1]] := ff[1];
fv[d2[2]] := ff[2];
fpos := 1;
for pos to dim do
if fv[pos] = -1 then
fv[pos] := b[fpos];
fpos := fpos+1;
fi;
od;
f := [op(f), fv];
od;
faces := [op(faces), convert(f, set)];
od;
od;
s := 0;
for k from 2^dim to 2^(dim+1)-1 do
b := convert(k, base, 2);
for perm in permute(dim) do
act :=
proc(v)
local w, m;
w := [seq(v[m], m=1..dim)];
for m to dim do
if b[m]=1 then
w[m] := 1-w[m];
fi;
od;
w := [seq(w[perm[m]], m=1..dim)];
end;
fperm := map(x -> map(act, x), faces);
s := s + pet_autom2cycles(faces, fperm);
od;
od;
s/2^dim/dim!;
end;
bs_Ninto_cind :=
proc(vN, ind)
local subs1, indvars, v, pot, res;
res := ind;
indvars := indets(ind);
subs1 := [seq(indvars[k]=vN, k=1..nops(indvars))];
subs(subs1, res);
end;
v :=
proc(dim)
option remember;
bs_Ninto_cind(dim, hypercube_face_cind(dim));
end;
This MSE link computes another cube-related cycle index.