This question has been asked many times with zero answers that I could find. Here's a hacky partial work around for 2D plots where a single axis fills the full figure window. It will add a line from the bottom-left corner to the top-right so when MATLAB crops the figure (without asking) it will have no choice but to leave the everything alone.
hold on;plt(reshape(axis,,2),'-w');hold off;
Assumes background is white and manipulates the current axis and figure. Would be great to see MATLAB address this problem (or point out an existing solution).