Thorsten, it was a very interesting discussion, and you certainly made me think about some details. Normally, any serious discussion should have stopped when I mentioned free energy devices, hyperspace drives, anti-gravity and thrusters that somehow work with electricity and without having to eject mass.
But I think, we have, at least partly, talked past each other, and that's why we aren't able to agree. You are thinking about what a future ship could look and be operated like if the necessary technical gimmicks would be available (even if these are very unrealistic), but I'm talking about how a "given" science-fiction ship could be operated as simple as possible (not as safe as possible).
And I don't want to design my own ship. I'm not very good at designing, but perhaps I'll do it one day, and I probably could create a shape that would be more suitable for atmospheric flying - and for landing and loading cargo. Let's be honest: The shape of the Python isn't suitable for anything, expect, perhaps, as a battleship, and I haven't even started about thinking how it would have to look in the inside. So any serious discussion about the shape of this ship is futile! I chose the Python because I like it, because I have access to the 3D model, and because it is big and heavy, but not so big that landing is ruled out. When I've finished "my" technology, it would be no big problem to use it with other ships if somebody wants to do it, perhaps even a variant of the Space Shuttle.
As you say, the Elite physics are completely unrealistic, and little has changed with Oolite - the latter is intentionally very near to the original and I actually felt at home immediately when I first tried it. This strange physics are necessary because it's a game where much time is spent by "dogfighting". You couldn't do this with ships behaving like they would in reality. And the Elite/Oolite universe has much smaller distances and planet sizes than in reality - this is necessary because with real dimensions it would be very improbable to meet any other ship, so the player would feel lonely. So I don't criticise Elite, I just accept the fact that it is a game, not a simulator. Even in 1985, when I first played Elite (I was 17 at the time), I realized this and thought about what resulted in beginning my mentioned C-64 "simulator". But then, more important things took over my life...
Try to see my intentions this way: I don't want to build a space ship for FG that is as realistic as possible, but I want to use FG to test if a simple ship like I'm thinking about, would be possible (and learn how to make FG models and systems in the passing). I want to see, how fast my ship can go up and down inside the atmosphere without overheating the hull, how difficult it will be to land, if it's humanely possible to control a drop from 500 km manually, and so on. Much work will involve creating plausible (electric) systems - for example we will need to start a small low voltage generator to be able to start the high voltage generators needed for operating gravity and thrusters. This is the part I almost had finished on the C-64.
It's not a "vision" of space flight, I'm only kind of experimenting, and if it doesn't work how I hope it will work, I'll probably try to change the parts that don't work. When the ship is "outside" the atmosphere, every resemblance to reality will be lost completely, because it can simply jump to another position. It probably will never possible in FG, and thinking about how I would do interstellar navigation or navigation inside our solar system is not what is bothering me at the moment. Going up and, especially, coming down inside the atmosphere will be the interesting part - and the startup procedure...
Your are, of course, comparing my "thing" to the Space Shuttle, but both probably won't have anything in common apart from cockpit windows and a landing gear. That's less than the Wright Flyer has in common with the A380. My ship won't have to go fast, it has unlimited fuel, it won't need external infrastructure, and it doesn't need wings because it has vertical thrusters and gravity drives. It will be flying more like an airship than an airplane. And, most important, it wouldn't have to go into orbit, so it wouldn't need to do the really difficult part of space flight. That's why it can be kept simple, apart from the fancy technology bits.