The only thing speaking against a Dzeko transfer are the players' wages. Lewandowski earned ~1,5 Mil Euro per year. Dortmunds' first offer for contract renewal was a duplication, making it ~ 3 Mil Euro.
Dzeko on the other hand earns around ~7,7 Mil Euro in Manchester iirc. So, if they want to sign him, Dzeko either has to take a huge pay-cut, or Dortmund will have to put a new signing high and above everyone else in the wage hierarchy. I don't see both options as overly realistic, but heck, stranger things have happened.
Other than that, I fully agree. From a purely sportive perspective, the signing would make a lot of sense.