Two of the directions of 4-way intersections are totally blocked. "Space" preset.

Fixed with a variant of idea 3 by 2497caf

yes that's a bit intentaional as you cannot really do a rail crossing in minecraft. Or do you have any suggestions on this?

Hmm some nice idea. I'll see what is possible

Some ideas:

1. A somewhat complex redstone-based auto-switcher All it needs is 5 torches, 4 detector rails, and some redstone dust:
2. Offset all of the north-south tracks to always be higher than the east-west tracks. The tunnels are big enough that you can stack 2 and have them fit. IMO, this would look best if you made the lower set of tracks 1 block below the current height, and the upper set of tracks 2 blocks above the current height.
3. Have the tracks temporarily cross over and under each other
4. Have the tracks turn instead of going straight