Your ideas sounds great. Unfortunately, as you stated, Stars Beyond Reach is keeping our beloved game devs' busy for now.
I never though about players' trains. It sounds like a big feature, maybe hard to balance.
My personal opinion about train is that I hate them. I'm really sad about this, because on the paper I love the idea of routing/hijacking couriers, but in the facts, tractors and widows trains stealing my whole fleet on my home world is just pain and no fun.
I, too, had some ideas. Like making trains a tiny bit less absurdly undestructible and giving them a metal cost, making destroying them rewarding by scrap recovering. Moreover, as you said, their pathing is quite unclear. What about each station listing the name of the other stations they can send trains to, and displaying the full routes when hacked?
I know I'm dreaming. But while I hunger for Star Beyond Reach, I'm also looking forward to the next AI War extension.
TL;DR: I'm sharing your feeling about Astro Trains (at least on the main points
)