You know, taking into account that SGA series contracts probably into the way of using the main cast more between the two series, something I just thought of that would have added some more coherence to the series would have been to make much more use of the Guest Star contracts.
This might be messy to look at, but DS9 had a number of recurring characters that were slated as guests. Without knowing a lot more about the physical contracts themselves (which may have been negotiated fairly strictly) we do have characters like Dukat and Martok that probably could have been used better in crossovers. Heck, Marc Alaimo played the first Cardassian Gul we encountered on DS9. If TPTB were a little better at thinking ahead, Garrick should have been the guy who interviewed Picard in Chain of Command. They could have used his disgrace from that episode was reason for being banished.
There are certainly missed opportunities all over the place >.<