Dortmund under Klopp was far from bad at defending. His system exposes defenders more though (pretty much like any attacking based style) than how Jose sets up his teams which leads to his defenders being more prone to brainfarts than normal but apart from their last season, where they mainly struggled with converting their chances, they have always been a quite solid team. I think their main problem is - apart from their below par quality at the back - that they are missing a defensive midfielder like Bender used to be under Klopp. They got their libero/sweeper in VVD who should be very similar to Hummels, Keita who is similar to Dortmund Gündogan, a fluid front three just like in Dortmund (missing a big technical striker and hard-working who can hold up the ball though, but it is obviously working for them with Firmino) and some pretty average but hard-working fullbacks.
It's highly unlikely he'll win the league within the next 2-3 years though, not because he is a bad manager, but just that money, prestige and overall quality-wise, Chelsea/United/City will always have a big head start no matter what.