My ranking:
1. Act III
2. Act II
3. Act I
4. Random EP #1/2 (seeing as 1 is also included within 2, I treat these as the same thing)
5. Branches EP
All are amazing though, it's only the Branches EP that I'm not overjoyed about and even that's great.
In terms of where to start, even though I think they've got better and better with each album (within the story anyway), I do think it's better to start from the beginning and follow it through. Much more rewarding.