[Eruhen]

To my (admittedly non-expert) view, the multiple-origins theory answers more questions than it raises. By having the First and Second Age orcs be based primarily off of Maiar and Eldar stock, it provides formidable enemies for the Eldar and Atani to battle without having the ridiculous scene of an Elf or a Man fighting an Orc half his size or less. Then, over the course of the Second and Third Ages, Sauron could breed Men (specifically Easterlings and Southrons) into the Orcs as a way of rebuilding the armies the War of Wrath decimated. Also, the Orcs that sheltered from the Ruin of Beleriand in the Misty Mountains would naturally decline in size to fit their new lodgings in the 7000 years between the Ruin and the War of the Ring.

I also like the idea of there being 'high' and 'low' bloodlines in the Orcish race, corresponding to more and less Elvish and Maiar blood.