I don't encounter this issue numerous times have I completed an objective for a quest I had been yet given and it all seems to work out fine for me. Have you done a game reinstall since release (or whenever you purchased the game)? My release characters still suffer the same bugs however my newer 2 (one created after 1.3 and the other after 1.4) have not encountered any bugs as far as quests. Don't misunderstand I don't doubt you just think that those original characters will always be borked....best to make a new one now and yes I know it svcks but is the nature of the beast.
This is a 1.4 character. Fresh start. Fresh install. Vanilla Skyrim.
Frankly, I don't see how you have avoided this mess, but I'm pretty certain that if you were to start a new character and go randomly casting about, you would accumulate a list of broken quests. Not that I doubt you, but there has to be some reason that multiple people on multiple blogs, including this one, bring up the issue of unadressed and, most frustratingly,
unacknowledged quest bugs. I would bet you a new graphics card that, if you were to kill the target in "Repentance" before receiving the the quest, your quest would be broken.
Now, just tonight, I had "talk to Esbern", or whatever it was, pop up.... again. I've been finished with the main quest for a month-and-a-half!
"Become a full member of the thieves guild" Done did it. Quest is stuck.
I don't know if this one has been fixed, but solve the bridge puzzles in Skyhaven Temple without Esbern. Bring Esbern later and he just idles preventing completion of the main quest.
These are all cases where conditions aren't being tested when an objective is given and the quest gets stuck. I'm half tempted to restart again and see just how many quests I can intentionally bork in this manner.