Thank you for your open and honest feedback!
As you know the components of UI for ASP.NET MVC are server wrappers of the Kendo UI widgets and the same themes are shared by both suites. That's why the Kendo Theme Builder produces themes for both suites and there isn't another builder for the MVC suite.
Nevertheless, I have good news that we are working on a new theme builder for Kendo/MVC that will be similar to the AJAX one - http://themebuilder.telerik.com. The release date is not yet available, but I can share that the theme creation and modification are refined and simplified as well as you will be able to choose from predefined swatches.
Since your feedback is valuable for us, can you please post your requirements in the Kendo User Voice portal? So that your fellow developers can comment and vote for them.
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