Besides its somewhat quirky UI, the main problem I have with feedly is that it seems predicated on the assumption that you will more or less read through all articles, one by one, in order, and finish them.
That's not how I use reader at all. I leave thousands of things left unread, and yet google reader makes it quite easy to keep up to date with whatever I feel like reading at the moment, without getting bogged down by all the stuff I don't want to read. It lets me categorize stuff hierarchically, and then drill down to what I want to look at, and maintains unread counts for each level, easily visible all at once. It's easy to see what categories/subcategories have new stuff. It's easy to mark stuff as read/unread, one by one, or in bulk by category. Yadayada.
Feedly basically flattens and linearizes everything, and doesn't give any summary information, so I constantly feel unsure what's available without looking, and once I look, I quickly get lost in the undifferentiated flow of articles.
Of course Google reader also allows a more "feedly-style" one-big-stream mode of operation via its summary feeds. Except that it does a better job of it by allowing multiple different views, and provides summary information for all of them too.
And despite all that flexibility and power, Google reader's interface seems far simpler than feedly's... it's really just a tree-list-view thingy like we're all used to from a zillion apps, and everything just sort of works like you expect it.
It does all that, and because it's web-based, everything's always in sync no matter where you read. It doesn't have dedicated mobile apps, but it works pretty well on smartphone browsers (and even on dumbphone browsers, although it started to flake out during authentication a few months ago, presumably because Google wasn't keeping it updated).
So basically reader's about a zillion times better, with one glaring exception: it's going away... TT
[The closest free replacement I've found so far is "yoleoreader", which kinda gets the vibe right, although it's a bit rough in places...]