The new Reichstag, holocaust museum, cafe society in the old East Berlin neighbourhoods - the young people moved in because they were cheap neighbourhoods.
Give the Octoberfest a complete miss - most Munchen do. The city fills up with drunks from all over the world and is a complete farce. On the other hand Munich is one of my favourite german cities at other times - drinking beer neath the pagoda in the English Garden, spot on; sitting in the pavement cafes along the Leopoldstrasse in the early evening is not to be missed when the weather is warm.
They do have wine and beer festivals in every town and city throughout the summer, so try and get to some of the smaller ones. Johanesfest in the small town where my half-sisters live is amasing, everyone gets out into the streets and parties, the whole town. Google and see if any are on when you are there.
If you are driving from Berlin to Munich then Liepzig and Dresden are on the way. Stuttgart is a quaint city - in the old part anyway. It all depends how far you want to travel cos Czech Republic and Alps are not to far, indded Prague is nearer to Berlin than half of Germany.
Have fun and I hope we have a good autumn to make up for the shocking summer here in Europe.