I've tried it without the anonymous function, didn't change a thing.
Digging further into it, I've now pasted the content of the
prototype.js into the script.user.js, however it truly does need heavy
modifying.
(Actually, when pasting the code, an anonymous function breaks the
whole thing again...)

I am not at a point where at least the Prototype code will load and I
can use some basic functions, however many other don't seem to work
correctly (Ajax, new Element, update, etc).

The posting below brought me on the right direction I suppose.
Greasemonkey seems to do some funky things to prototypes in general,
it is not limited to the Prototype framework.
https://mootools.lighthouseapp.com/projects/2706/tickets/149-greasemonkey-support


Not sure I can fix this thing at all. :(


On 24 Jul., 21:24, qufighter <[email protected]> wrote:
> Try:http://mark.biek.org/blog/2009/03/using-prototypejs-with-greasemonkey/http://jimbojw.com/wiki/index.php?title=Using_Prototype_and_Scriptacu...
>
> I don't think you can do it using require, not exactly sure why, but
> you shouldn't need to add an anonymous function wrapper unless you are
> using @unwrap (or try pasting the source into your script to avoid re-
> download although it may need some modification)
>
> On Jul 24, 3:11 pm, Robert <[email protected]> wrote:
>
> > Hello group,
>
> > I'm trying to include Prototype into a Greasemonkey script, but have
> > not been successful so far.
>
> > Below is the script I'm currently using (basically straight 
> > fromhttp://wiki.greasespot.net/Code_snippets#jQuery_in_Greasemonkey_scrip...
> > ).
> > I've tried playing around with the Prototype version, chaning it to
> > 1.6.0.2, .1 and .0, and loading it directly from prototypejs.com, and
> > also from my own webspace, but no success.
> > I also tried to remove the anonymous function around the alert, no
> > joy.
> > The file is being downloaded into the profiles directory, and there is
> > no error message or anything pointing out what is happening. It just
> > doesn't work.
>
> > Interestingly, jQuery seems to work without a problem.
>
> > Any help appreciated.
>
> > Robert
>
> > // ==UserScript==
> > // @name          Prototype Test
> > // @namespace    http://localhost/
> > // @description   Test Prototype
> > // @include      http://localhost/*
> > // @require      
> > http://ajax.googleapis.com/ajax/libs/prototype/1.6.0.3/prototype.js
> > // ==/UserScript==
>
> > // Anonymous function wrapper
> > (function() {
> >         alert('echo');
>
> > })(); // end anonymous function wrapper
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