The main problems I see with GWT vs. a native Javascript solution (jQuery or others) are:
There is an additional process that separates you from your final product. You develop your app in Java and you debug the Java code, yet you release a machine translated version of this code. For a decently sized app I can't imagine that you won't need to debug the actual code running on the browser at times, and this is going to be a headache, since it isn't your code.
Since you write your code in Java you are limited to use Java libraries. If you find some JS library that you like it would be awfully difficult to add it to your GWT project, you may need to write a Java wrapper for it. If you are developing native JS you can just add it to your project.
JS is an awesome language in its own right, with a solid object model that is different than Java's. I have developed a few apps in native JS for HP webOS and was surprised to find that many of the preconceptions I had about the language were not true. You can write clean, efficient and maintainable code in JS as much as you can in Java, and if you take the time to understand the JS object model you won't even need to use a support library to mimic a more typical class/object model like those of Java and C++ on top of JS. Javascript's prototypes are pretty cool.
If you may ever consider releasing your app on mobile platforms, then a native JS app can easily be wrapped inside phonegap and have access to several mobile platforms, without additional effort. There is a GWT wrapper for phonegap as well, but going back to my first item, if you have the choice to work with the real thing then why choose a solution that requires translation/emulation?
Good luck.
