The change to the screen scaling is a big issue for me. I can live with the uglier looking controls, but in landscape mode, with the new version, I can only get full screen (with overlayed controls) or the tiny original GBA screen. With the older versions of Gameboid, I got a nicely scaled GBA screen in landscape mode that fillled most of the screen, but left some room for the virtual dpad to the left. It was perfect. I can't understand why the developer took away this feature.
Old Gameboid (nice):