A couple of weeks ago I posted about my own decision process between OneNote and Evernote; To skip to the end, the result for me was OneNote. Interestingly, Lifehacker started a thread asking people which tool they prefer. More interesting than the poll is the comments. Here are some comments that jumped out at me:
- Evernote is great if you are organizing lots of OTHER people’s content.
- OneNote is great if you are the one generating the content and need to organize it
- Evernote is a clear winner if you work at a lot of different locations or on a number of different platforms. It has a number of mobile platforms so that you can take notes and add items on the go.
- OneNote is intimately integrated with Office, making working with it a no-brainer. It is also tightly integrated with Outlook for tasks, calendar, and email.
Honestly, I’m still moving forward with OneNote. I am also considering getting it for my machine at work, so that I can get very familiar with the app by using it in both places. But I can also see how an undergrad or a more web-oriented project might work better in Evernote.
ProtoScholar 
As my dissertation project grown, I have drowned in OneNote. It is not a good tool to organize a huge mess of information. I wrote one chapter in it, but as I worked on sorting out all kind of info for all 5 chapters I had to switch to Evernote.
Are you still playing with the tablet? You may want to look at PDF Annotator, which lets you to make notes directly to any PDF as you would do on paper (withou the need to ‘print’ PDFs to OneNote, which only a supercomputer could handle for a dissertation project).
Evernote wins for me because of the multi-platform support. I constantly use it for notes made on my iPhone and notes I access from my iPhone, as well as emailing notes to myself that I can access via the phone or browser.
Strangely, I can count the number of times I’ve used their desktop app on two hands.
I used Evernote for too long, and though it’s excellent in so many ways, I found 3 problems serious enough that I moved away from it:
(1) Its organisational facilities are feeble. Flat tags, with no hierarchies. For me, it rapidly became a mess if used for anything organisationally complex
(2) It is a monolithic container without an exit strategy. That means you’re entirely at its mercy, with even your organisational structure embedded in it. (Yes, it has export facilities, and an API; but as things stands, you cannot produce an export usable in anything other than Evernote).
Onenote is somewhat better in that notebooks are individual files you can organise within your own filesystem hiearchy (though it still lacks a comprehensive export)
(3) Its editor is extrememely limited. (though they’re promising a webkit-based replacement)
I still think Evernote is a great capture tool. But for creating and maintaining a stock of information, Onenote works better for me.
I finished my dissertation using Evernote, Word, and lots of paper. I ditched Evernote’s endless stream of updates awhile ago for Zotero, but as you mentioned it’s just not good for notes. Onenote vs. Endnote was a tough decision, but what tipped me toward Onenote is that it’s better managing and searching pdf files. Evernote only shows pdfs one page at a time, and while it lets you search, it doesn’t highlight the search terms like Onenote does. But, I actually prefer the setup (tags/notebooks) of Evernote.