Firstly, thank you Michael for coming here two days in a row to face the potential pitchforks and torches. I think that the just knowing that you are aware of people's concerns goes some way towards making people feel a little better.
For me the issues is to do with choices. Anything that I would consider to be a good game has to have choices and consequences, and so far Elite: Dangerous has done that. Without choices, everyone would want to fly the ship with the big guns, the strong shields, the tough hull, lots of cargo space AND an immense jump range. The size of the galaxy is one of the factors that forces players to make choices - if you want a fully armed and armoured ship then you can have it, but the sacrifice is that it is going to take you longer to get to where you want to be. If you want fast travel, then you can also have that but you will have to sacrifice equipment on your ship.
The instant transfer takes away the need to make those choices, which overall lessens the game. Not to forget those players who have spent a lot of time grinding for the engineers in order to get a better jump range for their FDL or Cutter.
As for the 3D printing thing - I think the problem is that it's inconsistent with the lore of Elite rather than the possible science of 3302. Arthur C Clarke's 3001 gave a view of the future in the next millennium where technology is so advanced that it makes the suggested 3D printing of Elite look like someone whittling starships out of wood. Star Trek has long had replicators than can create food and spare parts, but for good storytelling it has limits - the "resolution" isn't as good as that of a transporter, so some parts still need to be manufactured in a "traditional" way. I would imagine that starships use industrial replicators to create hull plates and other components which are then put together, you don't just make a whole ship and the limit is there for good story telling. At the other extreme, Star Wars does not have anything like replicator technology / 3D printing, but the technology in that universe has been around for a long time which is why we get to see battered, patched-up ships. I've always felt that the lore of Elite goes somewhere in between the two - travel technology is better than in Star Trek, but communication over long distances is not as good. Also, goods have to be hauled from one place to another in ships. In terms of the ships themselves, we are closer to the Star Wars universe - ships are not always shiny-new, and in the stories of Elite, they are generally patched up (also in game - otherwise why does my 'Conda have wires dangling from the ceiling?).
I'm sure most players can see how small drone ships could be created in a ship hanger just from stored parts, but it seems like too much of a stretch for a whole ship with custom engineered components to be created this way and it does devalue the idea of your trusty vessel, patched up and restored after many battles but still in use. As for the argument about your ship being restored when you die, I just assume that the old ship is salvaged at the same time as your escape pod or remlok-sealed body - which means that those juicy engineered parts are available for you to install when the insurance pays out on your new ship. The "instantness" of that really isn't a problem as long as you don't pay too much attention to the in-game clock.