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RCI do not guarentee direct flights as per their T&CS. Your T/A should have made you aware of this fact.
You always have the option of booking a "cruise only" and arranging your own connecting flights and transfers.
One point to remember when booking the fly/cruise package: when sailing in the caribbean, alaska, asia, south america, you would fly out the day before the sailing and have an overnight stay in a hotel, plus get transfers all the way. In the case of european sailings, you fly out the day of the sailing and you have transfers included.
I've travelled twice on mariner and once on voyager in the med. I was very impressed with the whole package costs, as it would be more expensive if i was to do my own hotel and transfers. So really, you might pay twice the actual air fare and maybe not get a direct flt, but you do have the extras like the hotel. I hope this helps.
The probablity is that there are not enough seats for a large number of people to be accommodated in travelling from Manchester to Barcelona and if you are estimating say 100 plus passengers travelling then the best way to get them all there is via a lesser used route. Remember that everything is done in the most economic way. You can, as Brian said, make your own flight arrangements, we do that quite often, but you must give yourself enough leeway so that if there are any delays or cancellations with your flights that you can still arrive before the ship leaves because it will wait for its own flight arrangements but noot yours.....Nei.
But if you decide to cancel the flights now, remember you will be subject to an admin fee of £35pp and also subject to any cancellation fees imposed by the airline. So it is always worth doing your research beforehand - if you are adamant about a direct flight book it yourself! Barcelona is not a difficult city - a cab from the arirport is only €30 to port.
We love RCI but just lately noticed cost cutting in packages on anything apart from the cruise (e.g. poor hotels pre cruise and inconvenient flight times). We are on a Brilliance cruise in May travelling one way back from Barcelona and for the reasons I've noted booked cruise only on booked Easyjet direct flights home (taxis port to airport are apparently under 30 euros). We saved a total of £150 on our booking so definately worth seeing what other options you have. My experience of free transfers are organised chaos whereas jumping in and out of taxis especially in the US is far more relaxed.