About the Troll Lady 'Eigner', she had to do it, else she would be not respected in her squad. The bad Joker has compromised her position in the squad, and therefore has even endangered the whole squad. To save this situation, she had to leave the military or to kick his ass in such a way that everybody would know what will happen if they cross the boundary. She choose the second one, gaining respect from the other military personal, which made her not look as a female, but as a squad member who can kick ass, if necessary.
This is not about some femistic BS, but real human psychology.
Overall DMS and DF lacked things in different departments, but DF was definitely better. Also DF was not save the world, but to save Berlin and therefore the Dragons.
What DF made better was that you had a feeling of being a mercenary leader and you had a 'choice'(not really) of accepting a mission or not. They need more to build up on this, and have different 'Runs' that you can make or not, and also the ability to acquire more information for a run, to choose your squadmates better for the mission (They Stole a Million). Or even have the ability to influence the run, before the run with bribery and etc. Also more solo missions with different approaches would be good, with a little more of a film noir touch like BladeRunner. This should also mean a real good detective story behind the scene, that you have to really figure it out. Not just run from A to B to solve Q.
Naturally the main choices should also have real consequences. In case of the ghouls, it would be good that they would help to attack the mercenaries, in the defending of Kreuzberg.
Overall there is much unrealised potential that can be utilised in a Shadowrun world.