As a French native I would say: "Ça aurait dû être prêt vers midi" or "Tu aurais dû l'avoir à midi". The French verb "préparer" means something like "to make ready" so it seems awkward to use it in the case of something which should _be_ ready (prêt). My first sentence translates approximately to "It should have been ready at noon", the second one as "You should have had it at noon" (I don't think you can directly translate "by noon", but that's another question :p )
In the OP's propositions, the first and third ones use tenses that are really not used in French anymore, even in writing. I learned these tenses at school but I'm not sure how they're called now
The second proposition is the one that feels the most natural to me but it should be "que tu l'aiEs" and I would transform it to "Il fallait que tu l'aies vers midi" (meaning "you should have had it around noon", and removing the "préparé" which doesn't feel right in this context).
Another possibility would be "Tu aurais dû l'avoir préparé avant midi !" In this case "avoir préparé" indicates that you have made it ready in the past so now it's ready.
Hope I'm making sense and keep up the good work!
