Been reading all the posts on the ships, and am finding it all a little funny.... I see the ships as a free extra, and will get whatever I can from them. I would suggest people can do a few things that will help themselves and everyone else...
1) If you hate them, opt out using the wrench on the top right of the game now available..... Voila ships are done for you after the refresh cycle takes care of anything in transit...
2) If you play them, understand that people have real lives and will get to them when they do. If it is not quick enough for you, skip their port.....
3) I am making a list of anyone where my ship stays for more than a day.... when I send my next ships out, if I see these names on the list I replace them.... no judgement or emails - just take them off in future itineraries;
4) If I see a stop of one of my ships has been more than 24 hours, I skip the port....
5) line up all your boats on one farm in order of time to fill a container..... Always work on the one that takes the least time to fill (you don't have to use them all)
6) I like starting my ships in the morning - load as many containers as I can throughout the day - and always ship at night before I go off to sleep

A routine like this helps avoid missing the departure
7) Look at the containers and establish a priority for you. I always start with the chemicals, ore and metal containers as that is what I keep running out of...
And lastly, I don't worry about how many containers I have on which boat.... Just do what you can and avoid trying for everything all the time - it is extra stuff after all..
And don't pester people or get upset if someone doesn't move your ship along like you would like...