Flex/Silverlight have limitations like lack of support for mobile/tablets and plugins falling out of favor, while HTML supports new concepts like IndexedDB and WebSockets. Developing UI logic in HTML takes more time compared to markup languages like MXML and XAML. Web Atoms provides a more markup-based approach for developing UI in HTML similar to Flex/Silverlight, with component-oriented development, templates, styles, and pre-built controls to reduce development time.