I don’t call Xen a second part of the game since it’s shorter than your travel in BMRF. I hated the first time become it was like a new gameplay introduced (non linear, verticals elements, etc.) and finding my way to next chapters more complicated.
Althought Xen was even more empty than BMRF.
If HL wouldn’t have a quick save, traveling Xen would have been a pain.
Now I don’t think cutting throught jumping part and vertical elements is the key to make it more enjoyable. Those elements were Xen essence, things that make that world far more different from earth where most of the time your path is plain and on the ground. Since EP2 (antlion cave, mines) and Lost Coast, valve prouved us that traveling verticaly isn’t boring or fun.
I think making clearly visible objectives (more visible portals) or path (maybe play on color or materials) is the key to help the player without suppressing whole parts and giving him the impression of space.