The Web Projects themselves are simply containers for the code that you create and a mechanism for managing and building the compiled project.
Based on my experience, the controls generated by VS comply to web standards ... that being said, browsers differ on which standards they do or do not enforce and how they enforce them. For the most part, you have a high level of control of the HTML that is output from your page. The table structure generted by the navigation control id valid HTML - you may be wanting to avoid the use of tables in which case, that particular control might not be for you.
For the most part, when you have a complex control you will need to take what you get - the HTML that is generated may not be intuitive to you and your team but that is often the price paid for the time savings gained by using a pre-built control, particularly one that is intended to service the needs of a wide variety of uses. (The same can be said for most code/script libraries you use/buy/find)
Many controls offer templating that provides you with the ability to define a template for how the resultant HTML is generated.