Of course Stuttgart 21 is objectively a mess but Germany is big, there's more than just a handful of engineering projects at any given time. We brought a pretty substantial amount of LNG capacity online in just two years but that never gets any press compared to the latest airport chaos.
[1]https://www.reddit.com/media?url=https%3A%2F%2Fpreview.redd....
Trains are late because they run a demanding schedule, trying to serve every big city (this is not like France where everything is supposed to go through Paris, this is a country that unified late with many powerful regions who all want direct connections between them).
There is not one single issue with the German network. Yes, the multi polarity you mentioned is one of them. But that's not the main issue, really more a feature.
One of the issues is that early on DB wanted to continue to make money with cargo, so they insisted on having cargo (and other trains) use the same lines. Rather then building new lines that nobody else uses. This choice over long term degraded to a situation where lots of high speed lines are just major upgrades of existing lines.
That leads to the network not having as much capacity as it could have had. And you have ICE trains blocking lots of the tracks for other trains, and the other way around. And even if the ICE can go, it can't go full speed because some parts aren't upgrade enough. You constantly go from a speed line, to an upgraded line, to a normal line, to a city approach.
While its great that in Germany the ICE goes to the main station, unlike in France where Paris doesn't even have a real main station. It also leads to ICE trains having to use an excessive amount of the old city network. And there are always issues there. Just last week our train was lolligaging around the approaches to Hamburg.
There is also just a general maintenance issue, personal and so on.
That all said, having traveled threw Germany a lot with the train just in the last couple months, overall, I think its amazing. But could be so much better still.