There is already a thread discussing these two:
Paperwhite 2 or Kobo Aura
Both have reduce the need for page refreshes. Kobo promotes it as low-flash waveform, and it is a feature of the newer e-ink carta display the Kindle uses. I don't know if one is better than the other?
AFAIK, the Pocket integration of the Kobo is just an answer to the send to Kindle feature that Amazon have always had (you can save articles and email them to your Kindle's email address and they'll appear on your Kindle).
Apart from the Kobo's screen being flush, I don't see that it will be any more likely to get scratched than the screen on the Paperwhite.
If you are going to carry your ereader with you every day, some kind of cover to protect it is absolutely necessary. Even if you want to keep it in a case while you are actually using it, I'd strongly advise getting one to put it in while you are carrying it - that is actually when it is most likely to get damaged.
Those apart, I agree that the font customisation is far better on the Aura, and obviously if you want epub, it wins on that too. It's also smaller and lighter, so has a lot going for it.
On the other hand, in terms of screen quality and the quality of the light, I think the PW edges the Aura in both (see my post
here with a photo), but to be fair, it's possibly pretty minimal.
The only other point to consider is customer service. Amazon are by a very long distance much better if you have any problems, Kobo's customer service seems a bit lacking.
So..... unfortunately that probably doesn't do an awful lot to help you choose between the two! Personally I'm edging towards the PW because I value Amazon's customer service, but it's a really difficult decision, as the size, weight and font customisation of the Kobo is quite attractive to me.
Good luck deciding!