Think you would like the 12.2 over the surface pro 2. I have both and while the surface pro 2 is great because you can use pc programs/apps on it, the screen is smaller and the battery life isn't as good as the 12.2. Weight wise the 12.2 is a bit lighter but they are close enough that may not make a difference. Size wise the surface is smaller so would be a bit easier to pack in smaller bag. Have to say having both compliment each other for their different uses, the surface instead of a regular laptop because of portability and size however the 12.2 really raises the bar for tablets. For your needs as stated, I think the 12.2 would be the better choice as laptop replacement as long as you keep in mind that as an android based OS it has some limitations such as not being able to use pc programs. Most of the pc programs do have a tablet app counterpart so you can accomplish most of the same functions. However it is the best tablet to date that comes closest to being a full laptop replacement.
I have a micro 3.0 to OTG cable and use a PNY 128GB thumb drive to store stuff in addition to the sd card. I consider that to be essential for storage and is easier to swap out without complications.
For note taking I really like the 12.2 over any other device I have on any os platform. The larger screen makes it nicer to take notes at meetings, seminars, etc. Sorry my college days are so far back I can't relate! I would second the Papyrus app for note taking over Evernote or the S note app. No experience with lecture notes although it looks like it would be great. Update: I just got the lecture note app and have played with it. It appears to be more feature rich than papyrus which is really nice because it is not complex in tools or operation. I think between papyrus and lecture notes you would really be set for anything your profs throw at you!