ael = numel(A);
bel = numel(B);
if ael < bel
alen = length(A);
ridx = randperm(1:bel);
output = [A(:); reshape(B(ridx(1:alen)),[],1)];
elseif bel < ael
blen = length(B);
ridx = randperm(1:ael);
output = [B(:); reshape(A(ridx(1:blen)),[],1)];
else
error('Output not defined when arrays are same size');
end
Your task would be a little easier if you were not selecting according to the length of the smaller matrix, since matrix size is determined by the number of elements, not by the first non-unitary dimension (the definition of "length").
Perhaps you meant to write about vectors rather than about matrices? But if so then what if the vectors are different orientations?
Also, I was not able to figure out whether you wanted the smaller matrix to be shuffled or copied intact, and I couldn't tell if you wanted the outputs to be separate or combined sequentially or intra-shuffled.
