Use a cell array (or a 3d matrix) to store your different matrices. Use curly braces instead of round braces to index cell arrays. That is:
for i = 1:6
A{i} = [1+i 3+i; 2 6+i];
end
However, I would not use i as a variable name, as it is also the symbol for the imaginary unit. You're really asking for trouble here, because the matrix expression will work even if you don't define i, but will give you a completely different result. Witness:
clear i %i is not defined
A = [1+i 3+i; 2 6+i] %and the expression now refers to the imaginary unit
