Not going for an RTS like element seems like a huge missed opportunity to me.
Fleet management becomes much easier when it moves from the 2D sector map to an actual Homeworld-like view. This would lend itself very well for end-game fleet/asset managment and would show the true scope of battles then fought. Think mouse dragging, drag & dropping for cargo, much more intuitive movement in 3D space and quick RTS like orders.
Sure, realism is at odds here but it wouldn't be unrealistic to assume that a future technology could simulate a real-time sector in a 3D VR environment that a user can interact with.
Here is a video from the Limit Theory prototype that shows an RTS-like environment:
https://youtu.be/ilg8azR2JK8?t=40
The ship cockpits are indeed immersive, but once you are in a capital ship you want to control the sector - and seeing recent VR developments, simulations of ones surroundings aren't a far fetched thought.
If you truly want to cast aside the menu mess of in-sector asset management, this is likely the most intuitive way to do it.
I hope you strongly consider the implementation of a view like this if we are indeed able to control fleets in X4, or create complex space empires.