Its my long time experience that it comes down to what you want to use them for. I have used NTrig pens on Lenovo's 1st (and only) pen tablet. It worked fine for long while, until lenovo stopped updating it, and i never felt like rooting it. NTrig does have to use a AAAA battery, sine Wacom has a patent on the non-battery magnetic tech. Yes, the HTC Flyer was kind of meh, but i've also used the NTrig on a newer Viao. So as far as writing or art, its close if not identical to feel as a wacom. Just that battery is tough to find sometimes, and not really cheap.
I recently got the Note 12.2 as well, and am loving it. I love doing digital art, and use this as a giant digital sketchbook. A Surface Pro falls short in a few places for my needs. And it has nothing to do with the tech or battery life. (the latter could be better) Using windows art programs on a portable tablet, without a keyboard, would slow me down. Buttons are not big enough to quickly change menus or tools. Pinch to zoom and pan are clumsy if included at all. And windows 8 is still unintuitive and annoying. By the same token, i have a Lenovo Thinkpad laptop i draw on as well, so i can always take sketches from one, and clean them up real nice on the other.
If you were using it for mostly notes, and wanted the MS Office atmosphere, then i think either is perfectly fine. Get a nice bluetooth keyboard for the note with a comfortable case, and baby, you got a stew going. (and potentially cheaper than the Surface's neat but expensive magnetic keyboard.) And a neat little tip, if you do want to make the arts, get a matte screen protector. (also sometimes called anti-glare) It has a bit of texture to feel a little like paper. And i got the SPen with eraser for the note 2 to use with the note 12.2. Its about the size of a regular ballpoint pen, and pretty cheap on amazon. I would just recommend changing the rubber tip to the plastic one if you're using a matte screen. Rubber feels weird, like rubbing a balloon slowly.