Wow, I really appreciate the amount of time you put in your comment. Thank you so much for this detailed feedback.
On your first point, I completely agree with your thoughts on expandability. I had started to prototype a shield generator car and a laser train, but disabled them before uploading to meet the competition deadline. I love the idea of junctions that you can shoot a lever to choose which path you go down. I think that adds a lot of meaningful choice in how the player progresses, not just coasting on one rail the entire game. It is funny, but if you are able to survive long enough in the current build (~60 minutes) you will reach the extents of the game and reach the null void where the background becomes grey. It is actually kind of a cool feeling going between those two zones, even if it wasn't intentional, so I think your idea of biomes is spot on and definitely something that should be pursued.
You also make a good point about the train braking. Early in development I found it useful so I could not miss an item chest, but as difficulty was tuned more and enemies were added, it became meaningless as you mention. My current build of the game I've actually already replaced it with a 10% self heal that seems to feel a lot better, and helps smooth out some of the difficulty spikes when huge waves are spawned.
With regards to detail/contrast, I'm a programmer by trade so all of the art assets I created were a best effort attempt while trying to minimize the chance someone could notice my drawing errors lol. I think I'm slowly improving, but I definitely recognize I have a lot of room to grow, and a more complete version of the game I would probably want to contract a real artist to replace the assets I had made. I do like the idea of introducing fog, and more particle effects in general would probably help sell the atmosphere while also bounding the camera extents as you mentioned.
On your last point, I had originally planned on having the train be expanded over time, say after every boss fight you could get a new train car added. That obviously was cut for competition reasons, but it is still something I am playing with. Early versions I had actually been testing with trains that were 20 cars long and it felt pretty awesome, but it definitely becomes even more difficult to control. I really do appreciate folks feedback with regards to the control scheme and this is something I am thinking very seriously about to try to resolve.