@jip On the "initial ferry transport dying" problem: Perhaps making it so the transport can build or special ability spawn the invisible and intangible ferry controller beacon? You then select the beacon and set up your route like normal, and have transports assist it.
As for loading whole fleets of transports, some variant of the ferry command seems like it would work. Using the same behavior that sends all the units to an appropriate transport, but then the transport just hangs out instead of ferrying.
Transports are my favorite part of the game. Making them more useful and viable would be the best.
I used to play the game SOLELY by setting a patrol route from a factory, having transports assist the factory, then moving the patrol route to attack places or retreat. Obviously not PVP viable, but it really makes you feel like a general! And the idea of 'platoons' that automatically get reinforcements is awesome.
I would also like a "wait" command that I can issue that just does nothing and everything waits, so I can cue up their overly complex flightplans and attack patterns, then cancel the wait command so everyone goes at once.
Oh, and orders contingent on other orders. Actually if the whole order system could be touring-complete that would be great.