DWR takes care of converting your Javascript objects to Java objects, and vice versa. If writing that sort of thing is appealing to you, you'll be very happy with Prototype.
Yes, Prototype certainly does offer things DWR doesn't, effects being one good example. But DWR's AJAX approach, which is markedly different than Prototype, allows you to continue to "think in Java", per se. You don't have to worry about how a given URL maps to a given Java class, and ultimately method. You don't have to figure out what call semantics and protocol to use to tell your servlets how to execute some method of some object. You don't have to worry about converting the return value from those methods into something your client can understand, JSON perhaps, maybe XML or something else. DWR handles all of that for you.
You stop thinking about servlets and requests and responses entirely with DWR, you simply think "at this point in my code, I need to execute method A of class B", and the fact that class B exists on the server doesn't mean a thing any more (other than not doing something that takes a long time when the user presses a key for example, but that's the same concern you have with *any* AJAX library).
Prototype is nice. I like it myself and have used it. I've even used it *with* DWR in the same app. But DWR's approach to AJAX is fundamentally different than Prototypes, and most other AJAX libraries out there, and it's that fundamental difference that has to be understood to see why one versus the other might be the right choice.
-- <br />Frank W. Zammetti<br />Founder and Chief Software Architect<br />Omnytex Technologies<br /><a href="http://www.omnytex.com" target="_blank" rel="nofollow">http://www.omnytex.com</a><br />AIM/Yahoo: fzammetti<br />MSN: fzammetti@hotmail.com<br />Author of "Practical Ajax Projects With Java Technology"<br /> (2006, Apress, ISBN 1-59059-695-1)<br />and "JavaScript, DOM Scripting and Ajax Projects"<br /> (2007, Apress, ISBN 1-59059-816-4)<br />Java Web Parts - <a href="http://javawebparts.sourceforge.net" target="_blank" rel="nofollow">http://javawebparts.sourceforge.net</a><br /> Supplying the wheel, so you don't have to reinvent it!