The Dataset - i think this part should be rewrited.
setSource - Primary Source - require some examples.
addCache - Caches - same, require some examples. Much more :)
Model data and methods. "In a typical ORM implementation, model data is stored in model properties while reserving all the property names beginning with underscore. Agile Toolkit stores model data as array in a single property called “data”." - add more low level explanation or stay on high level only. I think description set(), get() functions is more then enough at this point, most of the users will never ask you how it works behind the curtains.
class Model_User doesn't have public $table property.
"Please note that model is defined using PHP language and it’s always defined as a class." - i get confused with this phrase :) really :)
* you must define some fields* - how to define fields? Short example required here.
$m['name']='John';$m['daily_salary']=150; - why this written in one line?
* Extend “User” model to create “Manager” model.* - example might be very useful here.
Loading and Saving models - pretty good!
Relational Models (SQL) - this is h3 element. Everything "described below" has h2 element for header. Not clear what exactly is "described below".
http://book.agiletoolkit.org/agiletoolkit-overview/model.html