1. Programming Language: The first major difference between Plotly and Shiny is the programming language they are built on. Plotly is primarily built on Python, while Shiny is built on R. This means that users familiar with Python would find Plotly easier to use, while users familiar with R would find Shiny more suitable for their needs.

2. Data Visualization Library: Another significant difference is the data visualization library that each tool uses. Plotly utilizes its own open-source JavaScript library called Plotly.js for creating interactive charts and graphs. On the other hand, Shiny utilizes the ggplot2 library, which is a popular data visualization library in R. This difference in libraries affects the types of visuals that can be created and the level of customization available to users.

3. Ease of Use: Plotly and Shiny also differ in terms of ease of use. Plotly is known for its user-friendly interface and intuitive APIs, making it relatively easy for users to create interactive visualizations. Shiny, while powerful, has a steeper learning curve and requires a good understanding of R programming concepts. So, users with minimal programming experience might find Plotly more accessible.

4. Deployment Options: When it comes to deployment, Plotly offers more flexibility. Plotly charts can be deployed as web applications, embedded within websites, or shared as standalone HTML files. In contrast, Shiny is primarily designed for deployment as web applications using the Shiny Server. This distinction in deployment options can influence the way users choose to share and distribute their interactive visualizations.

5. Support for Machine Learning: Plotly has more extensive support for machine learning algorithms and tools. It offers features like built-in machine learning dashboards, support for TensorFlow, and integration with popular libraries like scikit-learn and PyTorch. Shiny, while capable of implementing machine learning models, does not have the same level of built-in support and lacks some of the advanced features provided by Plotly.

6. Community and Documentation: The community and documentation surrounding Plotly and Shiny are also different. Plotly has a large and active community with well-maintained documentation and numerous examples and tutorials available. Shiny, being an R-based tool, benefits from the extensive R community and has its own documentation and resources. However, Plotly's community and documentation are generally considered to be more extensive and comprehensive.

In Summary, Plotly and Shiny differ in the programming language they are built on, the data visualization libraries they use, ease of use, deployment options, support for machine learning, and the size and quality of their respective communities and documentation.