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the 'difficulty' rating purely refers to the amount of aliens on the map, 12 sectoids would be the same difficulty as 12 heavy floaters.
progression thru the main story only influences the captain pod of a UFO.
The biggest factor is based on how many days have passed, the game expects you have have made new weapons, amour, etc by a certain amount of time and will not hold back if the player has neglected to reserach or make them.
Story mission make late game aliens more common such as the sectoid commander but they becoem more common regardless if enough time has passed.
as for difficulty, it random for the most part (the exception of terror mission which are always swarming) but they are also time related and 'swareming' mission will also become more common as more time passes.
So in short time is the biggest factor when what alien shows up and how many will be there
http://xcom.wikia.com/wiki/Game_difficulty_(XCOM:_Enemy_Unknown)
*cough* I was actually asking a different question, and that site doesn't help at all, and not only did I google my question, but I read a few forum posts about it, and even mentioned what others thought in my OP *cough*
A couple of things are gated on game progression - the replacing of one enemy type with another happens twice based on that.