I know this thread has been inactive for a while but just in case some is looking it up here:
Vaccination is not mandatory in Germany. If a pediatrician is being pushy then it is just him/her and has nothing to do with the law. We asked around for a more naturally-oriented doctor and she was very fine with delaying the entire vaccine schedule (DD had her MMR at 2 years instead of 1 year). My tip would be look for midwives who are more naturally-oriented (a good source is a birth center) and ask them for recommendations. A lot of pediatricians and doctors here tend to describe homeopathic remedies and suggest well-known home-remedies. They tend to give me prescriptions with the subtitle "if you absolutely want to but it is not 100% necessary, you can wait it out."
As for Kindergarten, we received a confirmation that we got a spot and they haven't even checked her vaccination booklet so I assume it is not a must there too.
The well-baby visits are compulsory depending on which "state" you live in. In general, all that is done in these visits is a weigh-in, a general checkup that the child is developing properly and a few questions to see if there are any problems that can be handled early (e.g. Autism). It is then entered in the child's "Gelbeheft" (yellow booklet). The doctor will then inform the Jugendamt (Youth Welfare Office) that this child completed this particular visit. If you don't go, the Jugendamt will not receive anything on the child and they will send a letter to remind you. If there is no response, only then they will send someone to check if the child is sill ok/alive. Like others said, this is done so in response to abuse cases. A friend of mine got such a reminder because her doctor's office forgot to send the notice to the Jugendamt.
In Germany, kids are very rarely taken away from parents. Even in relatively bad situations they're kept with their families unless literally their life is in extreme danger.
The only thing that is compulsory here is school. No option of homeschooling here!