I have never read a yuri, and am rather new to this genre. I would prefer a plot that doesn't solely focus on the "yuri" aspect that has a good mix of things going on, but I will take whatever I can get.
Aoi Hana focuses on more relationships than just the "main", they involve plenty of other interconnected characters including heterosexual relationships. Sasameki Koto delves into subplots that don't involve yuri though the entire conflict is about yuri love.
My all time favorite yuri: Husky and medley for having such a fairy-tale outcome, even though it is based on a real-life girlxgirl story.
You can find a lot of gems in the oneshots too, some favorites of mine are: