Hi!
If I'm not patient it kick my butts or hit on my nerves. So, I do everything to be patient and let the time it needs to load the transports. I place my ppl near the transport, select all of 'em and click to embark 'em... it helps to avoïd some headaches...!
I don't know if you play more against the computer or on the Zone. As you surely knows, seas are an obstacle and you have to take the control of it.
So, when it's done,(it's just a matter of patience), load the transports, send trimeres with 'em. Secure the place(shores) with your trimeres to have a clean place to landing your troops there. (...or find the quiet spot on the opponent's Island)
I suggest to you to place same units in the same transport, also you can place priest and cats in the same transport.
Use ctrl 1-9 to assign a number to each gang you want.
--> With it, it's more easy to manage your troops after landings(if you have tons of units). Let your priests and cats behind the army during the assault; they needs protection, also you can assign a group to defend 'em.Remember ctrl 1-9 !!! !!Don't know if I say something that can help you, as you said that "is crucial to be able to handle transports efficently and fast. Both coming and going." - I suggest to you to rule the seas before making landings.
Also, when you rule on Island maps, place some of your trimeres (or war galley) near the gold of your opponent.
-->Most of the time the patches of gold were near the shores, so you gonna cut gold gathering of your opponent.see ya!