Here is my solution adapted from an old another to a similar question (simply transpose rows/columns):
%# input cell arrays
a = {'A', 'B', 'C' ; 1, 1, 1; 2, 2, 2 };
b = {'C', 'D'; 3, 3; 4, 4};
%# transpose rows/columns
a = a'; b = b';
%# get all key values, and convert them to indices starting at 1
[allKeys,~,ind] = unique( [a(:,1);b(:,1)] );
indA = ind(1:size(a,1));
indB = ind(size(a,1)+1:end);
%# merge the two datasets (key,value1,value2)
c = cell(numel(allKeys), size(a,2)+size(b,2)-1);
c(:) = {NaN}; %# fill with NaNs
c(:,1) = allKeys; %# available keys from both
c(indA,2:size(a,2)) = a(:,2:end); %# insert 1st dataset values
c(indB,size(a,2)+1:end) = b(:,2:end); %# insert 2nd dataset values
Here is the result (transposed to match original orientation):
>> c'
ans =
'A' 'B' 'C' 'D'
[ 1] [ 1] [1] [NaN]
[ 2] [ 2] [2] [NaN]
[NaN] [NaN] [3] [ 3]
[NaN] [NaN] [4] [ 4]
Also here is the solution using the DATASET class from the Statistics Toolbox:
aa = dataset([cell2mat(a(2:end,:)) a(1,:)])
bb = dataset([cell2mat(b(2:end,:)) b(1,:)])
cc = join(aa,bb, 'Keys',{'C'}, 'type','fullouter', 'MergeKeys',true)
with
cc =
A B C D
1 1 1 NaN
2 2 2 NaN
NaN NaN 3 3
NaN NaN 4 4