"I've now found out (and PLEASE be discrete if you recognise the school) that all the children that moved up with him to year 2 from that one particular class were not taught basic maths properly and need extra lessons to catch up."
Oh good grief, that's a real facepalm moment. Don't worry, I would certainly keep that to myself - to be honest, while it's terrible that your DS has had to put up with this, it's not totally out of the ordinary in the chaotic state bilingual system. DD1's Year 7 group (first year of Gymnasium) was a catastrophe for the entire class solely because of poor management.
"you're right that the teachers aren't sufficiently prepared for changeovers, in Berlin especially. Every new idea or system to do with school gets tried out in Berlin first!"
Both of those statements are so true, and really at the heart of the problem. Friends of ours chose a junior school about 9 years ago because it was trialling a new system and had loads of extra funding and extra teachers made available (and it was a pure coincidence that one of the teachers there was the wife of a certain well-known senator). It attracted more middle-class parents, got a good reputation, and was declared a roaring success by the education department and rolled out across Berlin. This new system was of course the Schulanfangsphase, which unsurprisingly didn't work so well when untrained teachers were expected to deal with a wide range of learning and age groups totally unsupported. Now, finally the senate has allowed heads to choose whether they use SaPh or not, and I think it's around 60% of monolingual schools have it right now (meaning that 40% have reversed the polics of just a few years ago). The head of our school flat-out refused to consider it and said it was incompatible with bilingual education.
The majority of parents are utterly fed up with all these half-arsed initiatives supposedly aimed at raising standards and encouraging disadvantaged children to perform better. These are worthy goals that I want to encourage, but the politicians keep on insisting that every school in Berlin does the same thing instead of targeting the measures (and funding) where they're most needed.
"I think it has slightly settled since then". Don't think it has really. There is still enormous conflict between the Senate and parents about the Zurückstellungen and Schulanfangsphase, the mayor of Berlin seems to hate the bilingual schools because they are elitist (that's true, actually) and the Europe School system is constantly under threat. Berlin schools are finding it enormously difficult to find teachers of any sort, let alone the best teachers, because they refuse to pay the same rates as other Bundesländer (last year DD1 was in a German class of 34 - that's actually illegal - because the school couldn't find another German teacher), and it seems to be a spectacular challenge to find good headteachers or deputies because they are appointed when they pass certain exams rather than because they have the best personalities and vision for the job.
On the other hand, British schools are equally insane, but about their admissions procedures instead; we have no hassle about uniform; and I'm actually really impressed with the quality of what my DC are learning from individual teachers - the ones who seem genuinely committed to their job and like kids. They're learning at an academic level which is waaaay above what I was being taught at the same age in the UK 25 years ago. So it's not all bad. Oh, and we live in the best city in Europe too 
. That has to be some compensation.