There are a lot of great ideas already said, and I'm not gonna touch all that castration stuff with a ten-foot pole-cat (As the old folks used to say).
Back to the dilemmas and knuckle-draggers: Maybe this could be solved by difficulty levels. Make "Mr. X" so he can't be killed on Easy, make a warning on Medium, and no warning on Hardcore. The smart and experienced players will probably post all the tricky parts anyway, and they can just tell the new players (I just hate the "Newbie" word). Then everybody will be happy except the programmers-sorry, guys.
I don't know about plagues, it seems too easy when you conveniently run into three plants just after a witch tells you about them. But it may be confusing if there were all kinds of plants and you had to find one and only one.
But I love the idea of being able to pick sides among factions, prove yourself, and even be able to accept surrender (if I get XP). Then I could play again and pick a different side. That would make the game much more rich and fun.
This could have concequences later: for instance if you help out a village of Elves and are named "Elf-Friend" later on Elves will be inclined to be friendly, and Dwarves will be inclined to be unfriendly (not hostile, just mouthy).
(One pet peeve that has nothing to do with this topic: the game's typeface! All the twos and threes look too similar in the trading screens and some other characters look similar.)


"In the last analysis, it is our conception of death which decides our answers to all the questions that life puts to us." --Dag Hammarskjold