I do agree with him on that matter. It looked good in the first version with the straight and than "crooked window", cause it makes the ilusion of a bigger sterncabin, the other way around, as it now, didn't work that well. I would still make the upper deck above the stern cabin two studs smaller (Keeping the Stern with the windows as they are now) and make larger curve with the "crooked windows". But that's quite a tricky build. I didn't master it to my liking, but maybe you find a way to do it :)
I would change the 2nd window (the straight one) into another gun port. I also would change the position of the Mizzen Mast (the one nearest to the stern). Move him two studs to the back (more aren't possible because of the steps.) It would be perfect, from my point of view, If you could change the position of mast and steps.
But in the end, all that matters is that you like your ship!