Linear w/ side quests A, B, C with optional side missions
Side quests come in two varieties and generally a game either uses one kind or the other:
Stapled-on, after-thought, content-adders to make the game less short. These quests are meaningless, and I lack motivations to do them. The only motivation is usually some sort of reward, which in turn throws off the balance of pursuing the main quest by providing your character(s) with experience and equipment. If you don't find a motivation to do the side quests then you will be unable to progress on your main "quest." If you do all the side quests because you're a gamer like most people, and don't give a shit about your character's motivations, then you'll have a normal, or easy romp through the main "quest."
Integrated side quests which make sense in the game world. You can find many examples of these in the "good" RPGs like Fallout and Arcanum. However, I still don't like these kinds, because the very nature of their sideness makes them unimportant. The only motivation for doing the side quests is, again, some sort of reward, which, again, impacts the balance of the game. The only thing that makes this variety of quest better is because consequences which can make replay more interesting. But that is merely a difference of being done poorly or being done well. Fallout and Arcanum feature integrated side quests mostly. Wizardry 8 and Gothic feature the former type of quest that exists in a vacuum.
In either case, I'm still opposed to the whole concept of "side" quest. It's either important or not. If so, you don't call it a side quest, it's part of the plot. Designers should stop filling their games out with side quests. I don't get to a town and want to solve everyone's problems, nor do I want to miss out on all the rewards that a player who does will reap. I want to pursue my character's motivation to solve the main quest without optional diversion (or the corresponding optional handicapping).
Non-linear aka sandbox, go do what you want
This is even worse. People revel in their freedom to ignore the main quest (even when it's a fucking daedric invasion). I reject the notion that the main quest should even be thought of as a quest. To a lesser degree in any RPG since Diablo, but conspicuously so in Oblivion, the main quest is just simply a long side quest where characters claim it's really important. It reduces the quality of the quest and reduces the motivation factor for the player.
Linear i.e. Do A then B then C
Sounds like a JRPG. They can be perfectly enjoyable. Your direction and goal is single-minded, but that doesn't necessitate that it is boring. This mode just lacks replay value, which really isn't something I look for in games, even though for developers it's an important value. If I had to choose between replay value or a well-done, linear experience, I'd choose the latter.
Of course, it also lacks options and opportunity, which can kill you if you're trying to roleplay a character you want to play, but if you accept that you're roleplaying Cloud the same way you'd accept you're roleplaying Avatar, you can see that all the choices presented in game (which you never get to make) are all consistent to the character.
Linear w/open world i.e. pick up and leave the plot as you wish
I don't really understand what this means. I can't think of any games it really applies to since I'd rather lump all the sandbox games into the sandbox category.
Linear with branching A,B then choose the C,D or X,Y path
This is perfect. This is exactly what I'd want as a player, since the sandbox shit doesn't make me motivated to do anything, and the side quest model that pervades almost all other RPGs is both retarded and leaves me feeling penalized if I don't do the side quests. Coming to a branching point would be awesome, because I'd feel like I had control over the story. I'd feel like my character would really be able to act his role in some way, and I would know that a person choosing a different path would be missing out on mine.
This structure would still make for a shitty game if the designers were poor. For instance, only ever giving you two paths (the C,D or X,Y paths), or making the path options too easily categorized like the good path versus the evil path, the fighter path versus the theif path versus the diplomat path, would result in a shittier game. But this structure done well presents the best opportunities for roleplaying and interesting narrative/plot of all the other structures done equally well.