I've been worried about find the feathers, but I've been slowly getting more and more from just stumbling onto them (so far 62, at the start of sequence 11). Also, when I get up on viewpoints, I look around in eagle vision before synchronizing- probably 50% of the time (at least), I can see a feather sparkling, sometimes even 2.
About flags vs. feathers, I don't know that it really matters to me. Before looking them up, went / will go through and search everywhere methodically (I like to go for at least 90% of collectibles before looking them up). In doing that, the flags were cool because I'd find a flag, then fairly quickly find another. Of course, that opens up more oppurtunities to miss something.
One thing I prefer about the feathers is it tells you what district they're in- I had some trouble in Damascus & Jerusulem (sp?), I think, because flags at area borders weren't clear as to which area they were in.