1. Architecture: WebdriverIO is built on top of the WebDriver protocol, which allows it to communicate with various browsers, while Nemo.js is built on top of the Node.js environment, providing a more robust JavaScript automation framework.

2. Flexibility: Nemo.js is more flexible in terms of test and spec organization as it allows users to structure their tests in a way that suits their project, whereas WebdriverIO follows a more structured approach for organizing tests.

3. Community Support: WebdriverIO has a larger community support, with more plugins and integrations available, making it easier to extend functionality, while Nemo.js has a smaller community but is continuously growing.

4. Syntax: Nemo.js uses promises and async/await for handling asynchronous operations, providing a cleaner and more readable syntax, while WebdriverIO traditionally uses callback functions for handling asynchronous operations.

5. Built-in Features: WebdriverIO comes with built-in commands for various actions like clicking, typing, etc., reducing the need for additional plugins, whereas Nemo.js requires additional plugins for many common actions.

6. Browser Support: Nemo.js primarily focuses on Firefox and Chrome browsers, while WebdriverIO provides support for a wider range of browsers, including Safari and Edge.

In Summary, when comparing Nemo.js and WebdriverIO, key differences lie in their architecture, flexibility, community support, syntax, built-in features, and browser support.