Everything reduces to one thing, if I'm understanding what you're saying: Yuri is overrode with cliches. The fact that most of the audience of Yuri manga doesn't seem to mind these overused cliches is one of the chief reasons why we get the same scenario over and over and over again. And in that, you are absolutely right.
But calling it "bad writing" just because Milk Morinaga refuse to ever leave the comfort zone? I would say that's going a little too far. Call it "lazy writing", sure, but the thing is, Morinaga's stronghold is not story, it's character building. And you have to admit that's done fairly good in all of Milk's works.
So yeah, your complains are all too justified, but that doesn't means it's bad writing. Originality is not what you expect from Milk's works, just like common sense is not what you expect from that NTR stupid parade that somehow got an anime adaptation
Still what heck... I loved Girlfriends and Secret Recipe. Those were great and well Girlfriends is probably what they're most known for. I honestly don't like this cliche. It is one of my most hated cliches in existence. I jokingly said,"Morinaga now we're a bad romance...You freaking sellout." Followed by mock sobbing. I can't express just how much I hate it. That's my thoughts anyway. I mean I'll still read it since I love Morinaga.