I pretty much agree with you VeloZer0, though I would like to point out that you can actually do stuff out of order in the original FFI (its actually possible to get the Job Class changes before you fight Marilith, if you know how...) but yes, I feel the real problem does come from games and their stories spelling too much out for the player. I kinda learned this with my GF, her experience with the series is with FFX and X-2 but she has been having the hardest time completing FFVI cause she is constantly getting lost and unable to find where to go next despite the game giving her instructions, she has not even gotten to the WoR yet. I sometimes wonder if we take our foresight for granted and quickly forget how taxing some of the early JRPGs really are.
As for side quests being logically silly cause you're trying to save the world, this is only amusing cause the majority of games only open up most sidequests at the end of the game after your party has been swept up in the doomsday scenario. Whereas logically, it would make sense to have a diversion when your still in the first half of the title getting tossed into minor problems that eventually snowball into the Doomsday scenario. V and VII did this beautifully
So I don't see them being terribly silly as much as utilized poorly by designers who feel they need to design for endgame as opposed to fleshing out the whole title.