There are so many things that were wrong wtih the prequels, but in the interest of brevity, I'll sum it up by citing the primary failing across all three: they failed to accomplish their purpose.
What purpose was that you ask? The saga of Star Wars in its entirety was intended to be a story of one man: the rise, fall, and redemption of Darth Vader (Anakin Skywalker). The last half of this was done in the first three movies, where we saw the great evil that was Darth Vader, a man willing to destroy entire worlds, and who in the end, gave his life to save his son and stop the greater evil in the galaxy.
Now the prequel trilogy was intended to set up the rise and lead into the fall; it was to show us the great hero Anakin once was; someone who fought for good and justice and had the admiration of the people (as well as the audience). When we saw what a great hero he was, it would make his fall all the more tragic to witness, making that ultimate fall a moving and evocative emotional experience.
But here is where it failed: in these movies, Anakin was never a hero; he never really ascended past the level of whiny brat (like father, like son I suppose, but at least Luke grew out of it by the end). He never demonstrated any heroic attributes or personality. His only redeeming qualities were a talent for the Force and skill with a lightsaber, and a shiny sword does not a hero make. The point is that he was never a character the audience could really care about, and as such, when the fall eventually came, it was less of a tradgedy and more of an inevitability. Whether this was the fault of the writing, the acting, the directing, or a combination of all three is up for debate, but ultimately what matters is that it failed miserably. It is said that good cinema moves the audience to emotion; the Star Wars prequesl simply moved people to apathy.