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Is there a performance difference between writing java inside jsp pages by embedding them in html (like php, and asp.net) -and- using controller classes and using the JSP page to render the data?
Both should be equivalent, since everything you wrote in a JSP (scriptlets I mean) is translated into a servlet class, so it will be equivalent. Of course the difference will be in the quality of the generated code and the code you manually wrote.
However, it’s not recommended to use scriptlet based JSPs anymore, you should use an MVC approach with scriptletless JSP and servlet controllers.