Pdf is a terrible format for anything really, let alone ebooks its an end format not easily converted into something else. each line of text on the page is a line it doesn't have a concept of a paragraph. It only seems to know the order that text was added to it. e.g if you had 4 bullet points added as 1,2,3,4 and later edited to read 1,4, 2, 3.
translating to another format becomes 1,2,3,4 again.
Having more than 1 column of text converting becomes a block of text where the first line of column 1 is followed by the first line of column 2 followed by the second column of column 1. in other words an unreadable mess. Sloping text is even worse as it will be read at 90 degrees and so the highest word on the page becomes the first word and again a jumbled mess.
epub on the otherhand uses xml which is pretty close if not identical to html and so can be reflowed to fit the screen fairly naturally, it also supports css, it knows the difference between bolded text and a chapter heading the main difference between reading in a web browser is that an epub will be laid out as a screen full of information at a time instead of scrolling down. Because of the h tags a page can be broken easily into sections and a heading can be placed at the top of the next page. you don't get a heading at the bottom of a screen and the body of the section on the next page.
One nice feature is that converting a html web page to an epub becomes incredibly easy. You can save a web page complete and then load it into sigil and most of the work is done for you or you can bring it in to libre office save as an odt and then save as html and then bring it into sigil. The reason for doing this is to localise the hrefs for images. Otherwise the images would be linked to the website they came from rather than local to the page. Now instead of having a pdf designed for A4 paper you have a document which is easy to read be it on a phone or tablet or computer monitor, good luck trying to read a pdf on a phone on a bus or train or on your lunch break.
Another great thing is the ability to display svg graphics. Students will be able to relate to this you are in a lecture and you write like crazy making notes but they are paper notes, which you have to collate into ring binders you could type but then you need to sketch a diagram or a graph. and then annotate it.
There is a cool little program called write (cross platform windows linux osx) it lets you write on a graphics tablet and creates webpages of your notes. with svg files or top files you can convert handwriting to text with some success or just leave them as svg. The thing is they are ripe for bringing into an epub and instead of carrying a ton of notes around you can have a small collection of epubs for each class that you carry around instead.
The thing is you generally can write faster than you can type, it takes a little practice to get used to writing with a tablet stylus instead of a pen but once you have it you don't need paper any more.
There are some pdf's you can copy and paste from and recover a working document but it is more complicated than you would like. XML is much nicer to work with. Once you have figured out a workflow you will find its a lot better to use epub rather than print to pdf.
Sigil 0.8.0 was released last week, it's major change is it now supports python plugins which have great potential for extending the functionality of the program. The main development is done on osx with ports to other operating systems. There is a slight snag as apple doesn't let source be compiled for older versions of osx which means official builds are targeted for osx 10.8.x upwards, I made a 10.7.x build which is available through the sigil forum on mobileread.com as are versions for xp debian ubuntu and other platforms.