We were trying to figure out how to get from Naples, Italy, to Naxos, Greece on a specific day, and ended up getting a flight from Naples to Mykonos for 107 euros per person.We chose a "flex" ticket, meaning no change fees but pay the difference if you change the flight. This is why:

Naples (9:45 AM) to Athens (arrive 12:30); Athens (leave 1:50) to Mykonos (arrive 2:30) = 107 euros (before tax, fees, baggage)
Naples (9:45 AM) to Athens (arrive 12:30); Athens (leave 2) to Naxos (arrive 2:40) = 345 euros (before tax, fees, baggage)
Athens (2) to Naxos (2:40) = 109 euros (before tax, fees, baggage)

So, basically, the flight from Naples to Mykonos via Athens costs less than a flight from Athens to Naxos. Crazy!!!!

Ideally, we'd land in Mykonos around 2:30 and then hightail it to the ferry port to grab the 5:10 ferry to Naxos and spend an extra night there (we are already booked four nights in Naxos). I know getting cabs from Mykonos airport is difficult (we are OK with taking a bus). I know the ferry schedule could change. I also know the flight schedule could change. I know the flight could be late.

So I was looking into staying one night in Mykonos (we are a family of four) and everything is so expensive. At the end of the day, it would be nice to get straight to Naxos (but not 800+euros nicer - it costs $200+ more per person if we flew to Naxos, even though the first flight (Naples to Athens) is the same).

What are the chances that the flight from Athens to Naxos might become available to us, through Aegean? For example, if the change the flight to Mykonos to another day, might we be able to bargain with Aegean to head to Naxos instead? The pricing makes no sense. The flight from Naples to Mykonos via Athens costs less than the flight from Athens to Naxos.

What are the chances that we will be able to get a last minute booking in Mykonos on August 29 for one stinking night if we miss the ferry? Probably zero, right? Or $$$$$.

What if any options would we have to get from Mykonos to Naxos if we miss the 5:10 ferry? Probably nothing, right?

First world problems, I know. Any advice would be greatly appreciated.

Just so you know, ordinary Flex with Aegean Airlines/Olympic Air is carry-on only according to the new fare rules. To include checked baggage you need to book ComfortFlex. Athens to Naxos is a Public Service Obligation (PSO) route where all seats are sold as ComfortFlex, and fares are generally high. Naxos has a very short runway (900 meters), so flights are with ATR 42 aircraft with a max of 48 passengers.

The fare rules for changes with Aegean Airlines are below:
https://en.aegeanair.com/plan/fare-rules/
I’ve never had to change my reservations with Aegean Airlines, but understand they are fairly cooperative. You may have to make a phone call to get an answer.

Very helpful, Heimdall. We chose "flex" but paid 60 euros extra to check two bags (kids suitcases are teeny). It sounds like even if we wanted to swap to a flight to Naxos it would be difficult. I'm not opposed to a night on Mykonos but I can't figure out where to stay! I'm leaning towards taking a risk and hoping we catch the ferry. If the Mykonos flight lands at 2:30, and the ferry takes off at 5:10, that should be doable, right? I don't want to reserve a room in Naxos if we can't use it but maybe I will just do that anyway and even if we miss the ferry we can take the first one the next morning to Naxos.

Or, maybe I can just change the Aegean flight and drop the Mykonos portion and take the ferry to Naxos from Athens. The Athens flight gets in 12:45. There's a fast ferry from Rafina that leaves at 2:30 (we would probably not make that one, right) and a slower one that leaves from Piraeus at 5:30. That would be a LOOOOOOOOOOOONG day though.

I haven't looked at Aegean's site for flights, but might it make sense to fly to Paros instead of Mykonos? Paros is close to Naxos and much less expensive than Mykonos.

THat would be my choice NYLilly ... but perhaps not as many flights as Mykonos, and smaller planes?

Paros has a 1,400 meter runway, which allows larger planes to land than at Naxos. If you plan to go to Naxos but can’t get seats on their flights, have a look at the Aegean/Olympic and Sky Express flights to Paros. If you can get a morning flight that arrives by about 10:30 you will have time to get to the ferry port for the Blue Star that left Piraeus earlier in the morning and departs Paros for Naxos at around 11:30. Blue Star takes about 45 minutes to get from Paros to Naxos. There are later ferries throughout the day from Paros to Naxos as well.

if I were you, I would keep an eye out for changes/cancellations of flights and ferries this summer. Just when we are emerging from the Covid pandemic we are faced with huge rises in fuel costs. Essential ferries like the conventional ones that run from Piraeus to Paros, Naxos and Santorini will no doubt keep running, but there may be schedule changes and price rises, especially for the highspeeds.