Which flight to choose?

Is this VCE-ATH Sunday flight A3671? Note that the flight arrives in Athens at 1:35 p.m. local time, not 12:35 p.m.

Anyway, if your two flights are on Aegean/Olympic you will only have one ticket, your checked baggage (if you have any) will be routed directly to Santorini. As you are arriving from a Schengen zone, you wont have any passport control and you will go directly to the boarding gate assigned to your flight to Santorini

So 1h20 transfer time is enough. Anyway if Aegean offers it, they can do it. (and do it every day)

On the other hand, if you take an ATH-JTR flight with Sky Express, you will have 2 tickets and will have to pick up your checked baggage in Athens (if you have any), then re-check it on the Sky Express flight. In addition Sky Express may have a different baggage policy than Aegean.

So the best option is to fly on Aegean for both legs of your trip

The ATR72 is smaller than the Airbus A320 (around 70 passengers), it flies slower at 10,000 feet lower in altitude, it's one of the least polluting and noisy commercial aircraft.

In addition it has seats, windows, a pressurized atmosphere, a crew with a pilot and a co-pilot and landing gear!

So don't worry.

To quote Douglas Adams, "It can hardly be a coincidence that no language on Earth has ever produced the expression "as pretty as an airport". Airports are ugly. Some are very ugly. Some attain a degree of ugliness that can only be the result of a special effort."

Why is this a question? If you're on one ticket, book the one with the shortest stop in Athens, i.e. the 14:55 flight with Olympic. Do you prefer to spend time on Santorini or sitting in an airport?

If Aegean are willing to sell you the ticket, they think it can be done. It is an intra-EU, Schengen to Schengen transfer so I would not be worried about the luggage. And if your luggage doesn't make it, it will arrive with the next flight.

What about flight from JTR Santorini to Athens ATH. I have choice of Sky express vs Aegean airlines. They are either A320neo or A321neo so similar planes.

Is Aegean better than Sky express? Aegean costs $40-50 more than Sky express.

If $45 is important for you then go ahead and book Sky Express. They are not as good as Aegean and you will have to collect your luggage and re check it with Sky Express. We have flown Sky Express several times mostly because timing worked better. They are fine.

Now I am asking about a different flight from Santorini to Athens non stop so no need to check in again. Previous flight was Venice to Santorin in via Athens.

Sky express vs Aegean for non stop flight from Santorini to Athens. Sky express is $40 cheaper but is Aegean better?

Yes Aegean is better they have won a regional airline award for 11 straight years. Sky express is good Aegean is better.