Couldn't find a way to submit suggestions to Adobe for improving the product (which, in itself, might be a suggestion), so here are a few things I think would be good to see in the next version of ADE:
1) Searchable bookmarks...I don't know if this is really complex to do, or if there already is a way to do this, but I'd like to be able to search through the hundreds of bookmarks I have for my Property texbook to be able to find things more quickly
2) Be able to "write" on the books...Also might be really complex (and already available), but it'd be nice to be able to type notes on top of the text or in the margins (and then maybe be able to search these?)
3) Zoom out further...I can only zoom to 87% now but would like to be able to zoom out more
Assuming you also want these features on an ereader, Sony has them.
Using a Sony ereader, you can take notes using either a keyboard, your finger, or the supplied stylus. (The tracking on the stylus isn't perfect, as the reader will sometimes pick up your fist & the stylus simultaneously & try to make a weird word out of the shapes from the two.)
You can also add bookmarks, and view them.
Go to youtube.com and search for prs-650 to see these features demonstrated.
They make the Sony ereader approach being a very portable slate computer.
I don't know about searching the notes on your computer, but I think you can download them to your computer.