Slow MySql server - even on a super fast server
I think you should change your server parameter to optimize server performance, you can go through this Percona Wizard https://tools.percona.com/wizard 

Also you can refer a blog post http://www.mysqlperformanceblog.com/2006/09/29/what-to-tune-in-mysql-server-after-installation/ this shows what parameter to consider to get optimize server performance. 

I personally recommend that you should upgrade your MySQL server to latest v5.6 GA and start using it as it has lot of optimization and InnoDB improvements.