To understand why the president is such a weak position in Germany, think of it as a constitutional monarchy. Back in 1918 (that's less than 100 years ago, basically yesterday in terms of history) Germany was a monarchy. Then, when the riots broke out, the guys who would found the Weimar Republic intended to go for a constitutional monarchy, with a weak Kaiser who's just a head of state without any actual powers. But things got out of hand, one thing led to another and suddenly the Kaiser was exiled and they had to do without him. So they created the position of president, more or less a Kaiser, just elected. He had some reverse powers and that's it.
But in the Weimar Republic political chaos was the very common and so the reverse powers were used on a daily basis. After the war when the new constitution was written this was identified as one of the factors that caused the previous republic to fail and so they decided that the president should have even less reverse powers. And that's how we got here.
Also, the Constitutional Court is a very good check against parliamentary power. The judges there tend to have the most common sense of all courts and because they need a 2/3 majority to get elected there, party politics tend to be kept out of the process.