Apple Tablet Custom Mods : There is a company which takes Apple laptops and custom modifies them into tablet computers. You end up with a full OSX computer which is also a tablet computer, without the limitations of the iPad.
http://www.itablet.theplaceforitall.com/about.html
http://www.itablet.theplaceforitall.com/about.html
There are people who've also undertaken this modification on their own
http://www.fabiennemaurer.com/blogflo/?page_id=83
http://www.fabiennemaurer.com/blogflo/?page_id=83
and you can probably buy an old 500-700 MHz iBook for less than 300$US and get it modified.
I agree with you that the iPad is not set up to be a serious tool and the need to type on a virtual keyboard makes it less useful than even the Palm or Graffiti software from almost 15 years ago.
If you really want to make a PDF of handwritten notes, likes the collection of Edsger Dijkstra's handwritten computer science notes at the University of Texas (for example, http://www.cs.utexas.edu/users/EWD/ewd10xx/EWD1036.PDF ), the best way to do that is to actually hand-write your notes on paper and then scan them in at a later time.