1. I disagree somewhat with the difficulty-specific usefulness of certain runes over others that you theorycrafted.
2. Even if the order that runes unlock fit absolutely perfectly with the content that you face, it provides a non-dynamic experience that will be way too similar on repeated playthroughs, and it still isn't a very good reason why I shouldn't be able to choose what I want. It doesn't effect balance negatively, it doesn't effect other players negatively, it doesn't do anything positive except frustrate the individual.
3. What you said does not ameliorate the design conflicts that I outlined previously.
I don't feel like you're in a position to make these statements. I understand why you make them, just that you can't say how something effects someone else. Unless you're testing a large playerbase from both sides of the fence. Blizzard is obviously making a concession here. I'm not sure I really buy the response from Bashiok concerning the topic, but I don't really see why Blizzard would make the choice without some reasoning or data collected through extensive playtesting.
That being said I could really go either way on the issue. Choosing from a small pool of runes/abilities or having them roll out one per level in a predetermined order. Both sound like fine methods to getting the player their skills.