Why PDFs Suck

In the context of research for my courses, I often find myself sifting through hundreds and hundreds of pages of work. My task is to read all this material and to summarize it so that it can be used in a research project of sorts. The problem is when you are looking at any form of current events, you have little choice but to rely on journal databases. These are almost always in PDF format (though some offer HTML-based readers). The problem is that you want the flexibility of printing out the pages to peruse them, highlight the important parts, write notes in the margins, etc. PDF, being a read-only format, is essentially a digital paper replacement.

PDF's strengths do not lie in the consumer market, however. If it had been thought out properly from the start, PDFs could be a far more useful technology. For example, if I have a 10 page document, and I'd like to mark things down, I have no choice but to print it out. Acrobat Reader or a compatible software will not allow me to do any type of marking to the document. It almost seems like common sense to have this feature, though. In PDFs, there is the potential of an almost paperless society. Instead of me printing off dozens upon dozens of pages of text just so that I can mark it up, why not have a very simply highlight function which would allow me to digitally do this? I have no problem with reading on my screen, but Adobe has not thought through this option. It doesn't seem like it would be that complicated to be able to save your marked changes to the document in a database of sorts. Much as in the case of regular paper, the authors' works are semi-protected in terms of copyright legislation, and for those requiring the text for any sort of serious purpose are given tools to facilitate the task.

Journal readers are only part of the solution. I already have a laptop, and I don't really need anything that has OCR and a digital pen. A mouse would work perfectly for highlighting and marking up things. It should be simple to add comments to the margin of a PDF document, and yet nobody has thought of it. Why must I be stuck printing off all these documents just so that I can research efficiently?

[Update] So I was partially wrong about this. Adobe does include advanced markup features in the full version of Acrobat. The point is still valid, however. Why should I have to pay hundreds of dollars just to get some basic markup tools? I don't need anything else that Acrobat offers, and it seems like basic markup tools should logically be present in the free Reader app. Considering the popularity of the PDF format, especially in academia, why does Adobe keep crippling it because they feel that highlighting is a "premium" feature?