TL;DR
I suggest that we add bridges and tunnels to train rails for higher train throughput.
What ?
I suggest that we add bridges and tunnels to train rails for higher train throughput mainly at rail junctions / intersections and also to possibly go over and/or under factorio buildings and ground units and structures.
Rules/Specs for Bridges and Tunnels
In my mind, here are some of the basic, logical specs and restrictions a vanilla version of train bridges and tunnels should have:
[*] Tunnels can't cross
[*] Bridges can't cross
[*] Both have a limit to their max length
[*] Train speed while on a bridge or in a tunnel may be different than on regular rail.
-- By default I would say slower for the sake of game balance as a bridge or tunnel are throughput advantages.
-- However, logically thinking: a train wouldn't have the same wind resistance in a tunnel and I think would go faster....whereas, on a bridge, I would think
definitely slower being at a higher elevation (more wind), and also the real world need for speed limits on bridges as per load specifications.
-- More expensive and advanced versions of bridges should be available in the tech tree (eg. Wood bridge at the start > Steel Bridge > Steel suspension >
Tunnel bridge > Titanium bridge etc etc ... where the effective differnce between each bridge is the max speed a train can travel.
[*]Only one train allow on a bridge / in a tunnel at a time. Signals shouldn't be placed inside tunnel or on middle of bridge.
Example of Possible Use:
BEFORE:
(Total of 4 Greater than 2 point intersections)
(Total of 16 regular Intersection points)

- Before Bridges and Tunnels.jpg (981.35 KiB) Viewed 3660 times
======================================================================
INTERSECTION AFTER Using 2 Bridges + 1 Tunnel:
(
Total of ZERO Greater than 2 point intersections)
(Total of 10 regular Intersection points or
37.5% fewer points for jamming)
Why ?
To further expand what is possible for trains and extend the end game.