I hear you, and I have done some effort to at least mark "missed" quests (that would otherwise be completely invisible to you) as "failed" meaning that they will always appear on your log. This is a feature of the FDC mod: all "missed" quests will immediately show up as failed, so you know exactly where you went wrong, instead of being left in the dark.
My original intention was to develop a system where you can "revert" any choice from any quest, so you can basically "go back in time" and redo stuff... alas, I have little knowledge about the way Eek! handles their plot variables. It's a fucked up mess to look at, every time I go back to the code, anyway. But maybe, someday in the future, this might become a feature (no promises)