Yes, Bethesda sold the game on being able to follow questlines or just go around exploring, or some combination thereof, but it seems what most commonly breaks quests is exploring an area on your own before you get a quest to go there.
This realization forced me to change my play style to try to do all the quests first before doing further exploration.
Having to read wikis before doing things and follow quests rather than natural exploration (all to prevent bugs) made me feel like I'm playing a game, instead of being immersed in the world of Nirn.
I do that all the time, no broken quests from doing that yet. I am careful what I loot from trunks though. If it looks like a quest item (i.e. "Broken Amulet", "Little Fry's Sword of Flames") I leave the item alone, if it looks like a general item, i'll take it. I've emptied out entire area's before gettting a quest for them... i.e. like the cave the headsman sends you to, ug broken oar grotto or something like that... i've cleared that out before getting his quest, as well as the other side quest that takes you there, and no problems with them breaking.... i will note though, on both missions, the one your to kill isn't there unless the quest has started, but all the counterparts are. i've found over 200 areas exploring on the map, clearing them out as I find them, but all still seems to be going ok for me in that aspect.. lucky i guess?
If you stand inside your house and let the game run for 10 hours and then save, your savegame size will decrease significantly.
10hrs world time right? lol... probably doesn't work with "Wait" either i'm betting.