I've only played through Skyrim once, but when I did, I did everything. All factions, all sides, all DLCs, even killed the Ebony Warrior on top of Snowy Mountain. That was a very intense fight and one of my proudest gaming moments ever. For the sake of immersion, you are correct, if feels weird being high ranking of not the leader for many factions but Skyrim still pulls it off greatly.
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You can't do both sides in one play through