I'm with Andion as far as the official interpretation goes.
I would let Expeditious Retreat effect the base ground movement of most creatures. It would be worthwhile to develop a different spell to effect base movement of flying and swimming creatures. What does not work well is allowing Expeditious Retreat to effect flying and swimming speeds of creatures whose natural movement are not flying or swimming.
I would be against allowing expeditious retreat to double the swim rate of humanoids simply because it feels like they would have to do more than just double the speed of their arms and legs. It feels like you're crossing into the realm of the haste spell to me. In order to give a clear distinction, I would just make it a different spell to effect swimming and flying types of movement. This applies only to creatures with natural flying and swimming, like avian and aquatic creatures. Remember that magical movement is NOT enhanced in any way by an expeditious spell--it effects natural movement only.
As for polymorphed creatures, I would force a caster to cast an appropriate expeditious spell either for ground movement or flying/swimming movement. So, there ya go. That's my take on it.
It still feels increasing speed of flying and swimming take a lot more work. If I wanted to be a bit more difficult about it for my players, I might even require the expeditious flying/swimming spell to be a level higher than expeditious retreat.