With Gundogan, as it is with Hummels, the low price is because he only has one year left in his contract. Yes BVB should have been a lot tougher and firmer last year when Gundogan wanted to leave but ended up staying.
I was defending them but after reading the joint interview between Watzke and Rummenigge hosted by Bild I think at least part of the problems lies with Watzke and BVB management. Basically Watzke capitulated, saying "Bayern is in its own league, of course they wanted Hummels because he is one of the best CBs and there is very little we can do about it", something to that effect. I was shaking my head when I was reading the interview as I thought Watzke lacked aspirations and courage to compete with Bayern head on.
But that said, the underlying issue is that BVB can't compete with Bayern financially. They can't offer the kind of wages that Bayern offers and they don't have the same level of appeals within Germany that Bayern has. Yes you can be a tough guy if you manage BVB but you really have to come to terms with the reality.
Like Atletico Madrid (to a lesser extent nowadays), like Sevilla and many others, they will remain a feeder club to Bayern and other top clubs (including us) for many years to come.