Remove the Midi-Chlorians. Qui-Gon's senses should be proof enough that Anakin is powerful, we don't need a blood test. I don't mind the Prophecy, but it would have been much better without the Midi-chlorian explanation. This change to the lore also contradicts the view of the Force shown by Obi-Wan in ANH and Yoda in Empire.
We would much rather have Qui-Gon's explanation of the Force be consistent with the explanations given by Obi-Wan in A New Hope and Yoda in Empire, but with his character's own personal touches. Here are their explanations of the Force (which is not unexplainable magic, as most seem to understand it).
Obi-Wan : "The Force is what gives a Jedi his power. It's an energy field created by all living things. It surrounds us and penetrates us. It binds the galaxy together."
Obi-Wan's explanation seems to imply that the Force is universal. Midi-chlorians do not create the ability to use the Force, but other living things create it. Any being can use the Force with enough training, focus, and patience. Specifically, your ability to use the Force stems from your mind, not from the number of symbiotic organisms within your body.
Yoda: "Size matters not. Look at me. Judge me by my size, do you? Hmm? Hmm. And well you should not. For my ally is the Force, and a powerful ally it is. Life creates it, makes it grow. Its energy surrounds us and binds us. Luminous beings are we, not this crude matter. You must feel the Force around you; here, between you, me, the tree, the rock, everywhere, yes. Even between the land and the ship. Luminous beings are we, not this crude matter."
Notice how Yoda specifically made the contrast between matter and humanity. Yoda says that humans are more than just the sum of their cells. Explaining one's ability to use the Force through the results of a blood test means that the Force does boil down to 'crude matter'. He also repeats Obi-Wan's assertion that all life creates the Force.
The Midi-Chlorian explanation in Episode I specifically refutes the explanations of the Force given in the original two Star Wars films. In the OT, we could say that Yoda is the wisest and most powerful Jedi because of his faith, dedication, focus, patience, intelligence, etc. In the PT, we say that Yoda and Anakin are the two most powerful Jedi because they were born with the highest number of Midi-chlorians in their body. This is almost a Social Darwinist theory of the Force.
Qui-Gon says that without Midi-chlorians, life would not be possible and we would have no knowledge of the Force. Therefore, all living things possess midi-chlorians, and all living things should have access to the Force
The film would have been superior if the midi-chlorians were never mentioned, though. The Force definitely has changed since Obi-Wan described it in Episode IV (Lucas was trying to make a positive change, but hurt the films instead). In Episode IV, Obi-Wan comments: "When I first met your father, I was amazed at how strongly the Force was with him." In Episode I, this comment seems to have changed to "I was amazed at how high his midi-chlorian count was." The descriptions of the from the original trilogy imply that your ability to use the Force is limited only by the strength of your mind and will. Yoda makes it abundantly clear that NO PHYSICAL LIMITATIONS can be placed on the Force, including a Midi-chlorian count. In the PT, this is no longer the case.