So I note from my file saves (I keep 10 going and rotate through them) that they all vary in size, but some newer ones are smaller than the older ones (Some by even as much as 700k).

Is there a way to manipulate save file size.. maybe by how much loot or quests you have?

It's just the nature of the game that it naturally gets larger as the game progresses. Unlocked Locations, Current/Completed Quests, Spells Learned, Perks Unlocked, Items, etc. all contribute to the save file size. Unfortunately there's no real way to knock it back down to any great effect.