I opened this thread a few days ago, and thought "Obviously not, what a silly question", but after reading the comments and thinking about it for a bit, I sort of am.
Choices are great. Having the option of either doing the main quest or a side quest is brilliant. However, having there being far, far more side-quests than main quests isn't really good. You have games like Kingdoms of Amalur, which has a brilliant main quest (or at least appears to, so far), but keeps trying to make you do its relatively boring side-quests instead. That's obviously not wanted.
I think my point is that I like having the side-quests be completely optional side-quests. When the game tries to make you do the side-quests instead of the main quest, that's not really good.
At the same time, I'm not particularly fond of the side-quests being virtually the entire game, ala Skyrim. Skyrim is a lovely game, it's not that, but I'd like it a lot more if it had some more actual, proper quest-lines in it.