This should work. You will get more than one child if there is more than one thing plotted or an annotation, etc.
gu = open('gugu.fig');
gu_ax = gca;
lu = open('lulu.fig');
lu_ax = gca;
figure; % The new figure
P = subplot(1,2,2);
copyobj(get(gu_ax,'children'),P)
P = subplot(1,2,1);
copyobj(get(lu_ax,'children'),P)
gu = open('gugu.fig');
gu_ax = gca;
lu = open('lulu.fig');
lu_ax = gca;
figure; % The new figure
P = subplot(1,2,2);
copyobj(get(gu_ax,'children'),P)
P = subplot(1,2,1);
copyobj(get(lu_ax,'children'),P)
