These are more wishes for the engine rather than the game content; you guys make great space sims and i've no doubt TNBT is going to be engrossing.
My biggest hope is support for parallel processing, in the game logic and graphics rendering. Since the original X3 engine was released, cpu and gpu tech has shifted from getting faster to being wider, but X3 only really improves with single-threaded performance. In an ideal world i'd love to see TNBT be highly multithreaded, such that when the game begins to bog down on my quad core cpu, i can simply upgrade to a hex or octa core cpu and have the game use that extra power. If you guys are sticking with sectors or some other kind of non-contiguous universe (tho i'd guess even a contiguous universe would have to be broken down into chunks of some sort), then something as simple as batching the OOS logic for sectors into an individual thread for each batch would be great, as opposed to one monolithic thread that walks the sector list.
The same with the renderer, although in this regard the X3 engine did pretty well with shader complexity scaling, it'd be nice to see vertex complexity scale also (a LOD system of some sort, DX11 tessellation would be ideal but even good old fashioned model swaps work). X3 always irked me that a several hundred thousand poly station was rendered in such detail regardless of distance, further aggravating the single-threaded bottleneck on my cpu (hello using SETA whilst pointed at empty space).
In short i'd really like to see an engine with legs, that not only takes advantage of current-gen hardware, but remains able to take advantage of processing power gains later, unlike X3 which simply couldn't.
My other hope for change is with the interface. X3 essentially has it's own window system, complete with dialogs, popups, and viewports. If you're keeping that system then i'd love to see it expanded to provide one massive usability benefit of most windowed UIs, namely drag-able windows that can be repositioned and resized.
Another enormous usability improvement would be some kind of shortcut system, just for example give the player an actionbar and allow them to drag commonly used commands onto it. I don't mind hitting C 4 2 2 enter enter to send a ship to dock at my TL, but it'd be so much easier to just target it and click a screen/keyboard shortcut that does 'tell my target to dock at...' or even 'repeat the command i gave my previous target'. Likewise clicking a screen/keyboard shortcut to launch boarding parties sure would beat targeting my transport and hitting a 5 or 6 key sequence i've had to memorise in mid-combat. I hate to say it but take a look at World of Warcraft's macro interface, combined with it's actionbar system, and you'll see an excellent way to reduce the number of keypresses/clicks for commonly used actions.
One last request would be multiple unit selection without having to use wings. If two, five, or fifteen ships can all take a common command, it'd be nice to issue that command once to them all simultaneously. Dragging a box over them might be a bit of an ask, but a ctrl/shift selection modifier would be more than enough.
Bit of a long post i know, but regardless of the above issues, i'm very much looking forward to TNBT.
