Werder Bremen is a quality side and I would choose their style over Bayern's anytime. However they face serious problems and have failed, for the moment, to provide adequate solutions. Most of all I would outline:
1. Young and inexperienced defensive line, not particularly competitive as a unit. They miss Ismael a lot, while Pasanen is injured and GK is not always reliable. Plus their coach adopts a rather open formation, with one DMC (usually Bauman). As a norm, they will score a lot (their attacking duo is the most productive in Europe so far, I think) but also concede, which is obvious in their statistics. While their ability to create dangerous situations up front is outstanding, sometimes they don't seem that solid / balanced. I think it was Frings who has recently criticised publicly this feature?
2. Lack of depth at the bench. Missing reliable alternatives, it becomes complicated in occasions when the schedule is tight, playing 3 matches per week. The starting lineup will not change so it is usual for them to face fatigue after 60-70 minute. This situation was more than obvious recently, when they lost in Athens against Panathinaikos. They should have turned the match but since they missed several clear opportunities, they suffered in the last quarter of the game...