The caa numbers are accurate but don't tell the true story I'm afraid.
LEQ has been closed most of the first quarter of 2014 and the 2013 figures suffered similar fate from what I understand. The result being that NQY will see a larger proportion of the IOS traffic than it should as when LEQ is closed the flights are re-routed and ground transport laid on at the expense of skybus.
The route also suffers badly with fog at IOS as well as LEQ which also restricts flights and will have an effect on numbers. Just this last week flights were cancelled and passengers transferred onto the boat due fog at st Mary's.
Whatever the future holds for the route I suspect someone needs to implement code sharing or interlining and the ability to book through tickets. Perhaps Loganair could base some aircraft at NQY and operate flights under the flybe brand which would allow such bookings to be made ? And attract passengers from wider afield.
cs