There's a few ways to play this game, saying this as someone who has sunk nearly 1000 hours over the years.
The main bus strategy is one of the most popular, and it is highly efficient. However this sucks all the fun out of the game for me. It feels like just tacking on yet another section of the factory and everything is already mostly figured out for you. The grid strategy with trains surrounding each square is even worse.
If this is how you guys are playing and it isn't enjoyable, try just going full spaghetti. Half the fun for me is trying to squeeze in some new area and figuring out all the turns, underground belts and pipes, etc.
And the game really opens up when you get to Vulcanus. Most people pretty much abandon their Nauvis base other than for a few things like importing science.