Many thanks for your suggestions, which are all great. I think that the plan now is to fly to Heraklion as there are no direct flights from Dublin to Chania. We will then take a bus to Chania but due to the times of the flights, it looks pretty tight to take the last bus to Paleochora. So, instead, we may take a taxi from Chania to Paleochora and then on the way back use buses. This at least will get us to our destination in the one day!
I've literally - as I was typing this reply - received a quote from Spiros Taxis of €460 for return taxi fares from Her/Pal/Her. Could be a possibility. I also checked out hiring a car but that was €450 for 2 weeks, which is it's going to lie idle, would be a waste.
My last visit to Paleochora was some years ago and I did use the buses for the return leg and I agree that you can see a lot as you're that much higher up.
Looking forward to returning to Crete and in particular to Paleochora!