To take it further, how do you go on to effectively govern a country where, for example, 65% of people voted Yes, but independence doesn't happen because you're 1% short? A lot of people are going to be very unhappy that their votes had less value, particularly if the 35% skews older as it likely would. If a much smaller Yes vote was enough to keep the issue rumbling on into 2022, I think that situation could become very ugly.
Rather unusually, I agree with you here. A 65% threshold for 'yes' in a one-off referendum is manifestly unfair.
But at the same time there is an asymmetry that needs to be accounted for somehow: A 'no' vote can (and inevitably will) be revisited after a suitable time has elapsed. A 'yes' vote on the other hand is for all practical purposes irreversible: If Scotland does become independent, the practical difficulties involved in reversing that decision, say, 20-25 years later, would just be too great. There's also the issue that, while future events are always unknown and will always take you by surprise, there's a much greater uncertainty with a 'yes' vote: No-one will really know until the secession agreement is worked out what independence would look like. Both of those factors do merit some requirement for a 'yes' vote to be particularly decisive.
In fact I'd go as far as to say that the 2014 referendum was (like the Brexit referendum) incredibly badly designed: As far as I can see, David Cameron et al simply didn't bother thinking through the consequences of the rules for either referendum. However the rules (50% +1 vote either way is decisive, once-in-a-generation vote) were agreed and decided on and accepted upfront by both sides, so that's what we have to accept.
Personally, I'd be comfortable with something like this: A referendum on the basis of: A 60%-40% victory either way is considered decisive. Anything closer is considered indecisive and goes to a repeat referendum, say, 8-10 years later. In the event of a win for Independence, then the secession agreement is negotiated and once the Independence terms are understood, it goes to a follow up AV-style vote in which people order their preferences (1-2-3) between,
Accept Independence on these terms,
Renegotiate for different terms, or
Abandon (similar but not quite the same as
@najaB 's earlier suggestion). While no referendum design is perfect, I think that would answer the challenges of making sure a decision is decisive while being reasonably fair to both sides.
(And before anyone complains: No, I'm not contradicting my earlier posts in which I've argued for no new referendum for another 10-15 years. The difference is that the 2014 referendum was held on the clearly understood basis of it being a once-in-a-generation 50%+1 referendum, but the SNP decided
after the result - in effect - to unilaterally demand that the rules be changed because they didn't like the result. What I'm suggesting here is an agreed-up-front basis for the referendum which treats both sides roughly equally).