There are some useful tips for reading papers using Anki here: http://augmentingcognition.com/ltm.html

Scroll down to the heading "Using Anki to thoroughly read a research paper in an unfamiliar field".

I've used the paper method in the beginnings of my English study and it worked well for me. SuperMemo was a really great tool and I liked it very much. Managed to keep using it for maybe 10 years, and I'm still sorry that I've stopped when the program and its community were in decline. But the method and algorithm remain the best and it's great to see it's used in modern applications - not just Anki but perhaps in all major language teaching apps. The fact that this article made it to HN front page speaks for itself.

As for using it for scientific paper study - depends what you expect from it. Spaced repetition is great for remembering and retention of facts. When I'm reading a scientifi paper, I rather struggle with the basic understanding of it :)

Ahh, but if you could better remember everything you have understood, surely that would help with understanding the next paper!