Reference: Part I of the question, and Part II of the question.

My feeling is that Part II is purely a discussion question. I also find the motivation distasteful, though I may have misunderstood it: "Because the display was getting quite cluttered, I thought I'd post a second part to this question separately." I admit that I haven't carefully read Part I, but this suggests to me that it was also purely a discussion question.

In a comment on Part II, Gjergji Zaimi said "I feel that you just discovered, what's being repeated over and over: that MO doesn't have the right format for long discussions" and fpqc said "I [am] concerned about the discussion-y nature of the question and the fact that it was motivated by the other thread filling up". I agree with these, but Pete Clark also said "I find your question to be appropriate and interesting, and I look forward to reading the answers", so maybe it's not as clear-cut a bad question for MO as I think. Then again, maybe that comment was meant as encouragement since the question was being attacked in the comments a bit.

Deane Yang commented "I also vote to keep this question. If anything, MathOverflow should find a way to foster discussions like this." I disagree with that comment. I don't think MO should try to be a discussion forum.

For reference, here are two threads here on meta about discussion-y questions and why we discourage them on MO.

Quote from the OP:

The long paragraphs above notwithstanding, the pedagogical question isn't something I lose sleep over. But it would be nice to have a few concrete and systematic ideas to use. They would certainly help me to understand the subject better!

The above is clearly asking for concrete suggestions on a pedagogical issue. People can give answers in the usual way. If someone has an objection to some answer, there may be some hullabaloo in the comments thread for that answer. But that does not distract much, does it?

A mathematics-education tag might be appropriate. Again this question is probably better as community wiki. But of course, the OP is not an intensive MO user yet; so he might not have yet figured out stuff like community wiki and all.

That is not an algebraic topology question.

I was sincere when I said that I find the question appropriate and interesting.

When a leading mathematician comes to MO with a long, carefully written question, I feel that he or she deserves the benefit of the doubt. We have a lot more to gain by leaving the question open than by closing it.

However, if you have enough reputation to vote to close and you sincerely feel that the question is not appropriate for MO, then I'm not saying you should refrain from voting to close it just because the questioner is famous and eminent. However, you should take extra care to be respectful in the way you go about this. Calling the question inappropriate and/or starting a campaign in the comments is truly problematic behavior, which will make a lot people upset and uncomfortable.

The best way I can say it is this: the math overflow community is a subset of the worldwide mathematical community, not a rival community. Thus in addition to any local norms or ethics, we have to adhere to the longstanding customs in the mathematical community, which is to treat everyone with respect but to be especially respectful to those who are more experienced, more senior and/or more established than yourself. (In order to be sure to do this consistently, many veteran mathematicians raise their standard of politeness and respect to EVERYONE they interact with.)

As a prominent member of the MO community, I was truly embarrassed and ashamed by the tone of fpqc's comments to Minhyong Kim. Let me assure you that people notice this sort of behavior much more frequently than they comment on it here. When I mention MO to people that I know or meet in real life, they often make references to know-it-all undergraduates or want to ask me about one particular user. I have never heard "Oh, that's the site with too many discussiony questions", not once.

The exact boundaries of what makes a question too discussiony for MO are far from agreed upon, even among the moderators and the longest contributing, highest rep users. Indeed, the opinions of many individual users on this issue can be seen to be nonconstant functions of time: I know my own opinions towards discussion questions have become more nuanced. On the other hand, the guidelines for what concerns respectful and disrespectful behavior in the larger mathematical community are much more standardized and agreed upon. In my opinion, it is a much higher priority that these agreed upon behavioral standards are maintained and enforced on MO.

I have a response, but I guess I'll just shut up out of respect for someone more established/senior/experienced than myself and to avoid making Dr. Clark feel any more embarrassed and/or ashamed.

I'll just note: the moderators respond to all inappropriate behavior by users, when it is brought to our attention. We don't patrol the site 24/7, we don't see everything that goes on here, we're not Big Brother. If you have concerns about a user's behavior, email us with examples of what they have said.

I agree that this is not actually a question, and as such I've voted to close. However, I certainly agree with everyone that we should be careful to try to be as welcoming as possible to serious mathematicians because we want them sticking around.