The current upload process is too much unpleasant and inconvenient. Managing versions and releasing updates is even tougher. If you could do something like wordpress.org does, it would be great.
As a workaround you may try our way of uploading: we do svn checkout of the project to our development server (which has powerful connection) and then upload items via FTP to codecanyon/themeforest. This way even big files upload within few minutes. But I agree, it’s hard to say it’s convenient