Stage size for HD YouTube uploads?

I just finished up an animation with a stage size of 640 x 480px. After exporting the file as a .mov and uploading it to YouTube, I noticed a pretty big reduction in quality, as well as widescreen black bars on either side of the video. Upon further research, I learned that by exporting the video with the stage size set to 1280 x 720px, the black bars and quality issues are resolved, but the entire animation appears stretched due to the doubling of the width. If I set the stage to 1280 x 720px to start with, it makes animating extremely difficult because I have to get used to matching the size of my drawings with a stage two-thirds the size of my monitor.

Are there any good methods of exporting an animation with HD quality without stretching and without setting the stage to a rediculosly-hard-to-work-with size?

Thanks in advance.