I also use Google Reader in (nearly) the way you suggest - but I have simply subscribed to the "all new maths items" feed. It means that I see about 150 new papers in the feed each day but personally I don't find this to be a massive problem (except when I've been away for a week or so). I flick Reader into "list view" and just scroll down the titles, expanding to see the abstract when I think something might be relevant. The majority of authors choose their title well enough to make this work!

It doesn't take so long to scan this list and I know that on a regular basis I see things outside of the subject categories I'd normally focus on. So I do pick up combinatorics, physics and algebraic geometry papers that I'd otherwise not find if I just stuck to math.QA and math.RT. Starring is nice and quick for holding on to things I might come back to later and I maybe download one or two a day too.

I appreciate that this might not be the answer you were looking for but, much as I love tech, sometimes it's quicker and easier to make the organic bit of the process do a bit more work.