Isn't some of this due to different use cases? The need for the German government to have a train from Berlin to Bremen makes sense in a way that probably doesn't matter if you're not living in Germany, but having a train that connects on the various borders in a compatible way is harder to fund and requires all the other countries to generally agree to do it at the same time.
The likely outcome of a whole-EU train system is something like the US system where Amtrak generally hits the major population centers, but leaves a ton of the US behind because when you talk about Federal priorities, a train from Denver to Dallas isn't a huge priority compared to LA to SF or Boston to NYC. Obviously the EU system would fare better because it's starting from a better base, but it's emblematic of the tradeoff between bottom-up and top-down planning and investment for something like this.
The problem in EU is that most of the funding comes from the states so they want their own taxpayers to benefit first.
So there's not really any interest in selling tickets from Country A to Country C. Because country B has to put up with the traffic which is already resource-restricted. And they prefer their internal customers to get priority.
This way it will never end up as a reasonable alternative for flying. What's really missing in the EU is the ability to bypass cities. A train from Amsterdam to Barcelona has to cross right through the center of Antwerp, Brussels, Lyon (or a transfer in Paris through a horrible metro connection). It's not possible to have a direct train that bypasses all the cities straight to its destination. That would be a real alternative to flying. Considering the amount of flights between Amsterdam and Barcelona daily it's easily possible to fill a few direct trains. It's that stopping in every city center (without in-city facilities for high-speed tracks) that make it so horrible.
But anyway the EU really doesn't care about this at all and considering the huge construction durations they're too late for this to make a difference in climate change anyway.
The likely outcome of a whole-EU train system is something like the US system where Amtrak generally hits the major population centers, but leaves a ton of the US behind because when you talk about Federal priorities, a train from Denver to Dallas isn't a huge priority compared to LA to SF or Boston to NYC. Obviously the EU system would fare better because it's starting from a better base, but it's emblematic of the tradeoff between bottom-up and top-down planning and investment for something like this.