So I was playing Super Mario RPG and got to a point (near the beginning, not really a spoiler) where the mushroom kingdom was invaded by shyguys. There was a steady stream of them coming out of the castle, so it should be obvious that in order to stop this invasion we need to go and take out the main force in the castle. Is that what I did? Heck no.
See, this is an RPG. Big bosses and main forces will wait while I take care of small fry first. I avoided the main castle like the plague until I had visited every single house and cleared out the few enemies that were bouncing in place scaring people. Because I stopped in houses and defeated every static enemy I ended up with some items that would permanently boost my MP. I wouldn't have gotten those goods if I had rushed in, beat the boss while taking on as few flunkies as possible, and made all the bad guys run away. The people just wouldn't be GRATEFUL that way.
RPGs are great at this. Show something in the story that shows you probably won't be able to get back to this exact spot and it makes the players nervous about actually continuing for fear of losing out on things that they'll never be able to get otherwise.
I personally just think it's annoying to have to search everything all of the time just in case you won't be able to get things later, but what do you think?