I hope you don't mind me contributing a little here. I'm new to the EBook scene, but an old hand at software development and a wide range of hardware platforms.
I think you have to realise that what you're proposing, as an interactive tool, is a different class of device from an ebook. It is entirely feasable to develop such a thing, but the requirement for continuous network access, interactivity, user generation and alteration of documents means that you're talking about a tablet or laptop, not an ebook.
EBooks are characterised by relatively simple hardware that can effectively switch off in between the brief moments when the user requires it to do something. Most of the time, this is turning a page - the user might read for a minute or so, during which time the machine sleeps, then it needs wake for only a few fractions of a second to update the screen before sleeping again. This, and the simplicity of the rest of the device means that it is (relatively) cheap to manufacture even in small numbers, robust, reliable and runs for significant time on a small battery.
Wireless network access, writing changes to files and handling complex user input all require that the device's electronics are 'on' for more of the time. That affects battery life, but it also has knock on effects - heat, more complex software, less reliability and so on. If a user is to use such a device for 'serious' note taking, the processor also has to be faster so as not to feel sluggish - and again that affects battery life and component costs. If you want to see what's possible, look no further than a netbook. Changing to an e-ink display does not change the equation that much.
Your description is far closer to a netbook with a tablet screen than an ebook. As ebook electronics become comoditised the gap is (hopefully) going to widen further as ebooks become cheaper by remaining simple, fairly passive devices.
Take a look at this
touchscreen tablet netbook - it would be able to do much of what you require with the right software. Whilst it's battery life is poor, other netbooks are getting closer to 8 hours - and to be honest it would be easier to ensure your academic institution had charging points throughout than to attempt to develop a netbook that lasts for a day on a single charge. After all, for most lessons and study, students will tend to be in a small number of places - not roaming across open fields.