Linear sequels that carryover from one chapter to the next installment ARE problematic. The first is the broad spectrum of related outcomes that have to be accounted for in the sequel. Given just how many quests and relationships and cause-and-effect events, the amount of required programming would be astronomical. Second, there's the "import you character from the previous game" annoyances. Say in Skyrim you stop playing at Level 60. The generic for the sequel would be to create a _1st_ Level character and build from there. If you import your Level 60 character, you miss out on the growth of the character. Either EVERYTHING is way too easy, or else artificially modified such that 60 = 1 and take it from there. Last game, your character finished as a god. In the sequel, tackling a mudcrab is like taking on a Daedric prince. So what was the point of starting at Level 60? Alternatively, the designers could say, "We don't care if your character finished at Level 60. Here, he/she starts the game at Level 10." And now the player goes "Woah! That's heavy-handed!"
Any way you try to work it, it just doesn't work smoothly. Wisely, Bethesda figured out that it's best to alter the setting, either temporally and/or geographically, such that the player can't import that demi-god from last game. At most, the player-generated events will be recorded as footnotes in History.