The 3-0 scoreline gives the wrong impression about the game. Bayern were in control most of the time and has a lot more chances. The own goal they conceded made them a bit too nervous. They wasted some unbelievable chances. It was still 1-0 almost 15 minutes from the end, Bayern went forward with all what they have looking for the equalizing goal. Werder took advantage of Bayern's push forward and hit them twice on the counter attack.
Bayern has had two main problems this season, sloppy defence and ineffective attack. Makaay and Pizzaro are great strikers, but Pizzaro can be inconsistent and Makaay is starting to show his age (Although he still has matches where he can score from any chance given to him). Hopefully that will be solved with the sigining of Podolski
Their defence can give away the silliest chances and make the dumbest mistakes. They really need a defender who can lead the defensive line.
Of course they also need to look for a replacment for Ballack. I heard they signed a Paraguayan named Dos Santos, supposedly he's going to take his place.
Hopefully with the right signings Bayern can return to being a powerful force in Europe.