Thanks for all your thoughts.
While I have accepted the new charges for seat selection, I was bothered by the fact that they held firm on the charge at the time I checked in for the following two reasons: (1) it's a full flight and they would have released the up front aisle seats anyways; and (2) I don't think consider it to be an upgrade.
Perhaps because the charge is new, they haven't quite worked out the wrinkles yet. If they're going to release the seats anyway, why not give them to your preferred travellers. While I appreciate holding out to the last minute to release the seats may generate additional revenue, I think once you get to the 3 hour mark it's less likely to happen. The risk for Aegean holding out is that these seats will be released to whichever traveller arrives at the check - in counter at the right time. I think this is a missed opportunity by Aegean toward their preferred travellers. Perhaps there could be a proper balance here (maybe at the 3 hour mark the seats could be released to the preferred travellers when the check - in counter for the flight opens).
I don't consider these seats to be an upgrade. These are not premium seats in any way - they are not wider, there's no additional leg room, there isn't better service - seat 6c is no different than seat 26c.
I don't think there is a sense of entitlement here. These are not business class or premium economy seats, and these are seats that are going to be released anyways. However, if there is, I don't think it's unreasonable for preferred travellers to want to be a step ahead of the crowd for immigration/customs purposes and to pick up their priority bag.
Aegean continues to be my preferred airline when travelling in Europe. I find the staff to be pleasant and helpful generally, especially the on board crew.