The same could be said about the internet. Surely, a direct connection between every point would make the internet ultimately fast, better experience, etc etc, but this rapidly becomes a huge problem the bigger the system gets.

In fact, we already have a massive point to point transit system, and it totally sucks ie cars. As soon as you start to take a look at the bigger picture and consider all the variables, you start to see the utopia just isn't. Congestion, pollution, upkeep, management, infrastructure, it's all exponentiated by the point to point system.

The system most countries with decent public transport have is the hub/spoke model, where massive transports (trains, planes, buses) travel between hubs, and smaller feeder services (buses, light rail, taxis) transport people from the hub to the destination. No system is perfect, but this is as close to it as you can get.

I used to take the train every day, my experience was fine, I would argue that bad experiences aren't due to trains but due to poor investment and management.