If I understand what you want to do, you can assign values to the InputName and OutputName properties of your state-space models. Then instead of LFT (which just connects up the first n inputs), you can use the CONNECT command. CONNECT automatically looks for signals with matching InputName and OutputName values and joins them up, leaving other signals unconnected.
So, for example,
G1 = rss(3,3,3); % arbitrary 3-state, 3-input, 3-output system
G1.InputName = {'a','b','c'};
G1.OutputName = {'y'}; % Optionally, you can use a vector valued assignment
% These are automatically expanded into {'y(1)','y(2)','y(3)'}
G2 = rss(3,4,4); % 3-state, 4-input, 4-output system
G2.InputName = {'y(1)','y(2)','unconnectedinput','y(3)'};
G2.OutputName = {'a','unconnectedoutput','b','c'};
% Give the inputs of G2 names that match the G1 outputs that will connect to them
%(change the order if necessary, such as {'y(2)','y(3)','unconnectedinput','y(3)'})
% Likewise give the outputs of G2 names that match the corresponding G1 inputs
T = connect(G1,G2,'unconnectedinput','unconnectedoutput')
size(T) % 1-input, 1-output 6-state system
% T has input 'unconnectedinput' and output 'unconnectedoutput'
Have a look at
doc connect
And at this example: http://www.mathworks.com/help/control/ug/build-a-model-of-a-multi-input-multi-output-mimo-control-system.html
Hope this helps.
