Which you think is better?

Actually I'm not a native but this is MO!:

At the first sight, I thought that A was right, therefore better, but after some thinking I noticed that B was also right and easier to say. We can have the written form as this: Which, you think, is better?, with 'you think' as a parenthetic phrase.

Ok, while we're all opining:   B isn't a sentence.

If "which" were a relative pronoun then B would be fragment of a larger sentence such as "I'll choose the road which you think is better".

But in this case it's meant to be an interrogative pronoun, which means the sentence phrase is supposed to be a question, and in questions you must reverse the noun and subject.   You could, if you don't mind sounding archaic, make it "Which think you is better?".   In that case Rafee's commas are an improvement: "Which, think you, is better?", or even better "Which is better, think you?".

But if you don't want to sound as though you were born in the 1700s, you must preserve the verb-before-subject rule for interrogative sentences by using "do": "Which do you think is better?".

[Hypothetical reader:] Wait, you don't have to reverse the subject and verb.

Ok, in the spoken language we use pitch to indicate questions, so we feel free to make declarative statements into interrogatives by letting the rising pitch indicate the true meaning.   Even in writing, therefore, I wouldn't hesitate to write use "You do?" or "You think so?".   Still, it's what makes B ungrammatical; the "do" isn't merely a redundant verb, it makes the sentence into a question.