It sounds as though djsches travelled with easyjet on their Saturday flight. Last year my son joined us and flew Sat/Sat out of Luton but with similar flights timings and, yes, it was chaotic. If he joins us this year he is considering returning home on Friday which, similar to Manchester, has a later flight - he feels that he won't be missing out too much on time in resort and he has the double bonus of cheaper return flight and no hotel cost.
Whichever way you do it you'll really enjoy the experience. It may seem a little strange not being part of a package holiday but it's far more adventurous and although you have made this decision to save money I think you'll end up being bitten by the 'indie' bug.
Incidentally, the service offered by the airport taxi drivers is very good and delivering you to the boat after buying a ticket tends to the norm and sometimes it can be the difference between getting on a ferry or waiting for the next. On one occasion when getting tickets in Igoumenitsa (Saturday morning rush) the queue was so long that kiosk operator told everyone to board the boat and pay at the pursers office' which we did. Last September we boarded the ferry without tickets and ended up having a free crossing - a long story but we were very willing to hand over our €20 to anyone who was prepared to take it and issue a ticket.
This brings me to the point about frequency. The ferries sail every hour or so from very early to very late and are work-a-day ferries which means the only things to stop them is the occasional strike or bad weather.