EPiServer Web Controls are developed to work with the ASP.NET WebForms framework and you have limited control over generation of ID-tags in some cases. It is better if you use dotnet 4.0 which is supported in EPiServer CMS 6.
It is a lot of work to eliminate all bad html generated by WebForms Controls completly. You will end up rewriting everything and loose a lot of ASP.NET built-in functionality. If you use WebForms it is probably better to be pragmatic and more cost effective and accept ID-tags and a small view state.
A common approach to get rid of view state is to remove the global form-tag used by ASP.NET. A known side effect is that the right-click menu in view mode used by editors stops working and also some common third party modules will also stop working as expected since they use the form-tag to inject javascript. You will also get issues with XForms.
If you want better control of the generated html render your page the MVC way using your own extension method that extracts values from EPiServer properties.
MVC is not yet supported by EPiServer CMS 6 but will nicely integrated in a future release.