Here’s an idea - what if new side quests pop up as your progress the main quest?
Chapter I, Act I - you have a few side quests to do as you start. These are relatively easy quests as you are new to the game, but might be a challenge since certain skills are low. The usual stuff.
Chapter II, Act I - you gain an additional amount of side quests that weren’t available before, even if you’ve spoken to the same guy in Chapter I who gives you the quest now in Chapter II. Some old side quests from Chapter I are now closed off, to avoid a lot of available side quests stacking up and then in Chapter IX, you’ll have two dozen side quests you want to do but you never bothered with any of them in the beginning and thus we have this very same dilemma that you spoke of.
I don’t know if everyone would think this would be too restrictive and un-sandboxy, closing off certain side quests as the game progress. But I hope anyways that many side quests we get are related to the story somehow, and not just a disconnected quest you got from some guy you met on the market that has nothing to do with the story. This shady character could be gone by the time of Chapter III, or he’ll show up some other place with a different side quest, or you find him latter hanging from the gallows because you never helped him in Chapter II. And if you do help him (not just helping him retrieving some sort of “misplaced” sword, but a much deeper side quest thant that), although he seems shady, he might be a good asset for the story later on. So in that way, he would have connection to the story, but since he’s a side quest, he can disappear if you don’t find him before certain actions take place. Stuff like that, you know.