I don't like the "feel" of all this readying. I originally envisaged it as an occasional action people would use for occasional circumstances; as it turns out, it seems to be the default way of acting and the whole game involves remembering what actions ships have readied. Needs work.
I agree, and that's part of the reason why a lot of my comments have been about what you can do with readied actions. I think the reason that there's so many readied actions is because there's so many mechanics in the game that allow you to gain an advantage by manipulating action timing.
How about the following idea, which is used in a lot (if not most) wargames like Warhammer 40K and Warmachine. You don't have initiative for individual ships; you just have a turn for each side, and each player can just choose to activate their ships in whatever order they like. As far as I can tell, this would eliminate the need for pretty much all readied actions except in the following two cases:
(1) The player doesn't have anything to do this turn but expects to have something to do after the enemy acts. (e.g. readying weapons for the enemy to come in close, or readying repairs for when you take damage). But for this the game won't break if you don't have readied actions - the player can always just wait until his next turn.
(2) The "lowering shields to allow transporters" thing. Was the intent with this to make you drop the shields on both ships for a whole turn? If so that seems harsh - as you said, in your example the heroes were powerful enough to render the ship they were on "unattackable," yet not powerful enough to be worth dropping the shields for a turn to transport. Probably the best solution is to say that shields on friendly ships don't block transporters - that could be explained as the friendly ships just dropping their shields just long enough to let the transporter through (which takes such a small fraction of a turn that it doesn't matter.) If you still want to make it harder you could do that a different way, like having it cost extra AP, rather than the current clunky system.