I think the last statement is false. I believe this statement to be true:
- if the player avoids the side quests, then he will not be confused.
but I believe this statement to be false:
- if the player does not avoid the side quests, then he will be confused.
If your game does not have design flaws, you can have as many sidequests as you want, and the player will not be confused, because you will have made it clear what he needs to do to advance the main story.
I think you are imagining a player that assumes that everything he sees is needed to advance the main story, and therefore is confused. Because he assumes that all interactions are somehow connected to the main story. But in practice he will stop assuming this in the first 10 minutes of play, after he sees how many objects and characters there are in the world. And he will start playing like a normal human being, instead of looking at stuff that he does not care about but he must do it because it could be useful, and picking up up stuff that he does not care about but he must do it because they could be useful. And then he will start enjoying the world.
More in general… to someone who has not played Ultima 7, it is very difficult for me to convey the fact that there can be a different kind of puzzle: a kind of puzzle where the challenge does not come from using objects in non-obvious ways, or using objects for a secondary property, but where the challenge comes from the quantity of things that you can do. And it is difficult to explain the sense of fulfillment when you solve these “puzzles”. It might even not be correct to call them “puzzles” because, again, they do not involve using objects in non-obvious or uncommon or far-fetched ways. Maybe the best thing is to make an example. In Ultima 7, while travelling to a place to follow the main story, you reach a place and find a compelling side quest there, and you decide to start playing it; and then you get back to the main quest, and the action that you need to do is not an uncommon or unconventional usage, so it is not a “puzzle” in the conventional sense, but nonetheless it is challenging because you need to: travel to the right place, explore it, identify the right person or object among many, recognize that is the useful one in the current context and the others are not, and remember that you need to do that particular action, after you have been involved in a side quest for 2 days.
From yet another point of view: have you ever wondered why adventure games are dominated by humor in such a disproportionate way? In movies, how many movies are comedy? 40%? And in adventure games, how many are comedy? A much bigger percentage, right? So this needs an explanation. The explanation I think is the following: since adventure games are small worlds (relatively few object, relatively few characters) where must the challenge come from? it can only come from using objects in far-fetched ways (sell the bottle to the clerk because it is the only way for you to get a nickel; use the battery on the electric fence, and so on). But these kind of puzzles only work in a comedy game. It would be ridiculous in a drama. If you want to make an adventure game that is not comedy, it is very difficult to make puzzles that are interesting and not boring. That’s because, to make a good adventure game which is not comedy, it takes another style of puzzle; a puzzle where the challenge does not come from using objects in far-fetched ways, but from identifying the correct obvious thing to do, among a thousands of other obvious things which you can do but which make no sense in the correct context.