I currently have User SEO URL\'s set to Yes in OpenCart Admin.
System -> Settings -> Store -> Server -> User SEO URL\'s
I came late but my solution could be useful for others (tested on Opencart 2.0.3.1):
Open your MySQL console and run this query (change YOURDATABASE with your db name):
INSERT INTO `YOURDATABASE`.`url_alias` (`url_alias_id`, `query`, `keyword`) VALUES (NULL, 'common/home', ' ');
How it works:
The trick consists in adding a WHITE SPACE (' ') for the column "keyword", if you insert an empty string ('') this workaround doesn't work and the url rewriter will return again index.php?route=common/home.