Just because you can become leader of factions in Morrowind does not make that equal the ease by which you are GIVEN leadership in Skyrim and Fallout 4. Skyrim and Fallout 4 GIVE you these positions after minimal effort, and Fallout 4 even gives it to you at the beginning without doing anything - General of The Minutemen. Childrens' games have that kind of writing.
Morrowind and even Oblivion made do much more.
To Skyrim's defense... the factions that you end up heading up are much smaller in scale.
It's not like you become the head of a fighter's guild that spans an entire continent, or even region. At the end of the day, the companions are a rather sorry bunch. In terms of pure numbers, you're only the chief of a group about the same size as a Baldur's Gate party. And you don't recruit, if I remember correctly.
The thieves' guild is a bit of a ruin that you help rebuild... Only the mages college has a kind of 'impressive' thing about it. But even so, it's miles from the aura that the Mages guild had in Morrowind, with the teleporters from location to location etc. It's in a region hostile to magic generally, and doesn't seem to have much impact on local politics.
So yeah, you take control of them much too easily, no argument there. But they're really nothing to write home about...