Can craft omit default locales from generated paths?
In your config file you will want to define the locales such that en points to the root directory.

'siteUrl' =&gt; array(
    'en' =&gt; 'http://craft.dev/',
    'cy' =&gt; 'http://craft.dev/cy/'
 ),


And your public html folder should not include an 'en' folder:

/craft
/html
    /cy
        /.htaccess
        /index.php
    /.htaccess
    /index.php