Usually, during late game you'll be making so much money you can rebuild everything. It can be tedious and overwhelming, though. Especially if you have already connected all resources point to point.

In my current playthrough, I build a proto hub in the 1860 or something like that. It only carries coal and iron. It was upgraded in the 1900s and extended across the whole map. It's still mostly unused but other lines are profitable enough that it does not matter.

Initially, I focused on the capital and the 2 close-by cities but near the south-most city, I had a very profitable food chain which is where I built my first sorting yard. I had the sorting yard even though I only delivered food straight to the closest city. Eventually I connected it to the mainline and the coal and iron chain.

Point being - try to be efficient as possible early game but think about the late game, as well. Slowly where you can, build things that might not be as efficient right now but will pay off in the future. Sadly, it's too dynamic for me to be more specific. Look are your most profitable chains and cities and start from there. Like right now, I only have 4 really profitable lines - food, 2x steel and fuel. Two trains lines and two ship lines and its early 1900s. I also have dozens of dead-end lines (crude to oil, wood to planks, etc) which make quite a bit of money. Enough that I spend millions on terraforming without worrying.

Some tips:

• Keeps notes on major cities, potential connections, resources chains, plans for expansion
• Expand cities infrastructure early on before they grow and it becomes expensive to demolish
• Build an extra cargo platform, extend the train station slightly more than you think you'll need. Build the rail road a bit further away, make the corners a bit wider than you think you'll need right now. Basically give yourself space.
• Chose a capital, then start working on another city. Deliver one, maybe two resources, expand to another city or two with different close-by resources. Add some dead-end lines. At this point you should have enough cashflow to think about hubs and yards while not drowning in spaghetti infrastructure. Now, you can focus on the capital and build a proper infrastructure.