The problem with a 3 way vote of Deal , No Deal , Remain is that it fractures the Leave vote and if nothing is done about it, Remain might be in first place with only 34% of the vote. Similarly any "winner" of that would rob the other 66% of a voice and is illegitimate.
So there is talk of a second preference system. Where you vote for first preference, then a second. This however is an absolute stitch up because what Theresa May has done is deliberate negotiated a deal that is worse than both Remain and Leave. It is actually far worse for No deal voter (and remainers) because they are forced to express an alternative preference when they don't have any, because the deal is as bad or worse than remain. and for the remainers, any second preference means that they think they would be worse off.
I think the best way to run a second referendum would be to ask two questions.
The first question asks to see if at least 50% of voters would accept the deal on offer. If there is majority consensus , then the deal is passed and we have "Brexit".
The second question asks if the deal on offer is rejected, would your preference be Leave (w/o deal) or Remain.
I think that is the fairest way to frame a second referendum. What about your thoughts?