You can only challenge the final act, here the act of parliament, in other situations the decision of the highest court possibly involved, not, as a rule, mere intermediate steps, such as the voyage of a minister to an international conference or the acquisition of paper in order to draft a bill. But the waiting time you can spend usefully with collecting arguments or money.

The Federal Constitutional Court (BVerfG) has produced many silly and problematic judgements. It conceived of a right of informational self-determination, but unfortunately it has to be exercised in other peoples computers; it found that it doesn't matter whether you live off your savings (if only going through an annuity insurance) or continue receiving payments for work done perhaps decades ago – for me the coup de grâce for the capitalist order in Germany; and finally it felt that the right of the government to incarcerate people without anything resembling a proper reason should not be curtailed.

Perhaps this is another one. The court was not amused to learn that the MPs would vote away long established rights and freedoms because  they "were told so." Therefore it required that the parliament give its assent to each and any (if I'm correctly informed) legislative act of the EU. This will lead to an impasse, if the EU Council of ministers decide an act against the vote of the German parliament; if the court sticks to this interpretation, the EU majority vote would have to give way to the German opinion.

But this is still, fundamentally in my opinion, only half the way. The German parliament would still suffer from the inability to introduce bills (shared by the EP, which will, however, be of lesser importance under this scheme). This is of the utmost importance, because  in this situation the premium for all kind of lobbyist is increased: it is very difficult for the polity to react against a legislative act, however silly or one-sided it might be.

So this decision doesn't really point to a viable future for the EU, but only towards more complications and possible roadblocks. In fact, it might prove the death-blow for the European project.