The choice between Java Full Stack and MERN Stack depends on various factors. Java Full Stack is a good choice if you have experience with Java and prefer its strong server-side capabilities. It's suitable for enterprise-level applications and offers a wide range of frameworks and libraries. On the other hand, MERN Stack is a popular choice for building modern, single-page applications with a focus on JavaScript and React. Consider factors like your project requirements, team expertise, and scalability needs when deciding.