Autogsdoc and wiki syntax
The class documentation should have simpler syntax than XML. For example a wiki-like syntax, where references would be enclosed in [[ and ]] for the ObjectiveC message sends, one should prefix the first [ by a backslash. Like: \[[alloc] init].
Italics should be marked by ''italics'', bold by '''bold''' (mediawiki) or by __bold__ (phpwiki)
The references should be: [[Class:class_name]], [[Method:Class:methodName:]], [[framework:framework name in local documentation namespace]]
The requirement of specificaly marking instance variables should be reconsidered. Italics should be used instead. Firstly, it is already common. Secondly, there is no need to preserve an information in the documentation that specified word is a function argument or an instance variable. The information is obvious to the reader from context and already used different font.
XML is a bit complicated for such simple task as documentation. ack, I'd suggest something like ruby's rdoc