When you say the markup is not very good. What do you mean exactly?
We don't have a graphic designer, so I can understand the lack of aesthetic appeal. However, are you seeing issues with the CSS/HTML? How do you measure how well it works?
He's probably referring to the bulk of inline styling and javascript, and using tables for your layout. It should be fixed, but honestly the design has bigger problems than the code right now.
You should be aware of what a site does within a few seconds of visiting.