I'm going to have to agree with you regarding HUDs. Despite JB's hatred of removing doubt, there are multiple systems in place in the real world (IFF being a primary one) to tell your allies who you are, what you are, and where you are.
Allies will always want to know exactly what allies are where, and will always be attempting to deduce the exact same knowledge of the enemy. The enemy in turn does everything they can to either mask their presence (near impossible in space) or mimic something they aren't (very much possible in space).
Given that heat signatures are nearly impossible to hide in the vacuum of space, a ship is not likely to be concerned about emissions during flight. This means all allies can have information as up-to-date as information travels: for discussion purposes, I will be assuming all communications are instantaneous. I cannot imagine communication delays being implemented into the game, so this seems like a reasonable assumption. Given that communications can be encrypted and the communications are instantaneous, there is no reason other than "gameplay" for an ally to not know every detail of every other ally's ship, should they so desire, and as long as the other ship has not gone dark (waiting in ambush on the surface of a planet, perhaps).
Given that this information can be provided by something other than visual confirmation, it would actually make sense for every ship to be as close as possible in terms of profile. The more similar each vessel is, the greater the confusion enemy detection systems would have. If you have two ships, one being a half-scale model of the second, and place them at a distance where each is the same size to a third observer, there is no way to differentiate what is what without having to rely on an "active" system (using a laser beam to ping the distance, for example).
That all being said, it really does come down to "gameplay" as to how accurate the HUD values become.
I don't recall anybody asking for an autopilot, but I certainly hope any system has, at a minimum, on/off options.
I'm not sure that I agree with the phrase "runway" per se, but having a tunnel for generating initial velocity is actually not a bad concept. The faster small craft are moving upon departing the carrier, the faster they arrive at distant targets, and the less time the enemy has to muster a response. I believe I mentioned it earlier, where the carrier could essentially "fire" bombers or torpedo boats at enemy capitals/installations, instead of the small craft relying only on their own engines.