Arguably the biggest problem was that it was impossible to purge all the SED sympathizers from the schools and other public facilities
Not only that, but I think the overnight destruction of the DDR was a horrible mistake to make. I did quite a lot of research on the topic, including speaking to people in East Germany, and it's painfully obvious now that the West Germans didn't understand the attachment that people had to their state. To kill East Germany without putting it to a referendum was an awful idea - especially as the March 1990 election wasn't really fought on the issue of unification.
Had East Germany entered into economic and social union with West Germany as it did, but remained a partner to West Germany until the country had been stabilised (therefore preventing the abusive Treuhand practices and keeping the Treuhand under East German control), I think things might have been different. West Germany would have paid up to stabilise East Germany regardless, after all.
I'm definitely a firm believer that unification shouldn't have taken place until after elections in 1994 and until the East German people could decide without emotion. As it was, the process from around late April until October 3rd was like a runaway train.