There seems to be a lot of stick waving over in this thread, and it got me to wondering - why the *short * end? This is apparently to denote some sort of adverse relationship to the stick, and you’d much prefer to receive the long end of the stick, if you had your druthers. If it was a sword being waved at me, I’d MUCH rather receive the short end than the long end, as the short end is much less likely to tear me in half.
Warning! WAG ahead!
It sounds to me like a reference to drawing straws – i.e., the selection of who among the group is going to be the sacrificial lamb. Break the stick (read: straw) into unequal segments and force each potential victim to choose one blindly. He who got the short end of the stick was the winner…or should we say the loser?
To extend this WAG even further, the expression MIGHT have its origins in the Roman practice of decimating cowardly troops. Each group of ten drew lots (or straws) and the loser was beaten to death by his fellows. Perhaps someone else can confirm or refute this.
It is my understanding that the original expression was “the shit end of the stick” and it has been cleaned up for use in mixed company. “Grabbing the shit end of the stick” comes from the old practice of using a slit-trench latrine when setting up a base camp in the woods. After each use of the slit-trench, the user is supposed to cover their feces with a small amount of dirt and stir it up with a stick to aid in more rapid decomposition and keep the smell more under control. Typically, a sturdy stick is left stuck in the ground (or leaning against a tree) next to the trench for this purpose. This works out quite nicely as long as the stick stays upright and you can see what you are doing. But if the stick gets knocked over and you need to avail yourself of the trench after dark, the very real possibility of grabbing the shit end of the stick can be quite shocking (and unpleasant).
All this comes from my memory of what I read in an old camping book one time, and may well be a folk etymology made up of whole cloth. So take it for what it’s worth until someone can verify things for you.
SC
This has confused me since stick’s ends don’t have lengths. The stick has a length, granted, but unless you put some sort of divider mark on the stick you can’t say it has one short end and one long end. It could have a thick end and a thin end of course. But a short end of a stick seems as meaningless as the short end of a ruler;
I think it’s a combination of two phrases:
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Short shrift meaning a bad deal. when a military chaplain has a lot of wounded soldiers that need the last rites, yhe doesn’t have time to shrive each on4e fully, so he gives them short shrift.
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The wrong end of the stick meaning a misunderstanding or mistake. I think it comes from the days before toilet paper, when people used sponges on sticks.
I cry “bullstick”! 
Yeah, I know, horrible, horrible…
Here’s what I could find:
Lookks good but the source page is from a forum and I don’t have any other verification.
Obscure Reference Alert
I thought Sam Huff invented the phrasing… 
tremorviolet’s cite(by Christine Amer, Am. Hert. Dic. of Idioms) is correct. Her book is very well written and the info is factual. BTW, try NOT to quote huge texts from a webpage or a copyrighted book. Give the basics, then link to the source, as you did. But we’re all guilty of doing that sometimes.
Sam Huff was NEVER on the wrong end of a stick! After killing my Skins for years, we finally got him to come over from the Dark Side.
Warning: anecdata ahead.
I always heard this expression as “the shitty end of the stick”. “Short end” makes no sense to me, but YSMV…
Many years ago in Scotland, so the story goes, it was “the mooky end of the stick”. (They had neither toilet paper nor corncobs.) That certainly needed cleaning up.