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1a) “What is it?”
b) “What do you think it is?” (is it reversed)
2a) “What would be a good way to go about this?”
b) “What do you think would be a good way to go about this?”
2b apparently does not get reversed,maybe the awkward sounding “What do you think a good way to go about this would be?” is still grammatically correct but not used for the reason that it sounds bad. Or there is a difference between sentence 1 and 2 that has one reversed but not the other.
Questions formed by "what + be" usually ask for the subject complement of the sentence (or for the subject complement of the embedded clause):
1b) What do you think it is? -> I think it's an animal.
2a) What would be a good way to go about this? -> A good way to go about this would be to examine it thoroughly.
Now, notice that in (1) "it" cannot be the subject complement. We cannot say: * An animal is it. However, in (2) subject and subject complement are interchangeable. We can in fact say: To examine it thoroughly would be a good way to go about this.
When the speaker is faced, as in (2b), with a relatively long phrase next to the verb "be", he can seize the opportunity that the long phrase can be interpreted as either subject or subject complement and place it in end position (as a subject complement) to avoid a relatively long subject before the copulative verb in the embedded question, which would make the sentence sound awkward:
I believe you are misinterpreting the meaning of the sentences. Thus, the question represents a misunderstanding, rather than a difference.
Question 1.a: the question is being asked of the general audience, which would include the speaker. Question 1.b: is being asked in a more directed fashion, with the object being "you".
When you look at the phrasing this way, it becomes apparent that, in question 2, precisely the same thing happens. In 2.a, anyone in the speaker's audience, including the speaker, can answer the question. In 2.b, the question is directed specifically to "you". It is not asked in the question, but it may be helpful to realize that "you" may be singular or plural, one or many.
Also, the first style, where the speaker asks the question so that they can also provide an answer, is frequently used as a rhetorical device. In that case, the speaker knows the answer, or believes they do, and is seeking to make a point, or to direct the audience's thoughts.
Let's make them apples, instead of apples and oranges.
The two sentences are not related as written. I am not analyzing the second sentence as written because I think if you read what I say below, you will see there is in fact a reversal, when you compare two comparable sentences:
Based on 1a, you have a normal question:
"What is it?"
In "What do you think||it is?", the interrogative regards the verb think: what do you think, and not it is.
In order for the two questions to have parallel structure, sentence 2a would have to be:
"What would it be"? And the interrogative form with think then becomes:
"What do you think it would be?"
There you can see that What would it be reverses to it would be if you add a question with think. The reason is the same as for the first question: The question form concerns think and not "would be".
Now, both sentences in both forms have parallel structure. The straight question (reversed be verb) and then interrogative form with the verb think where the verb to be in second clause is not reversed. Both your examples now work the same way.
