The midichlorians make perfect sense if you think about what happens to Vader. As a whole-body person, he was supreme. The Emperor turned him to the Dark Side because of his power with the Force.
Then Obi-Wan laid the smack down on Mustafar, reducing his body mass (and, thus, his midichlorian count) by 50%. After that, Vader was a mechanical wretch, the Emperor's little whipping boy unable to live up to his full potential.
That's why the Emperor wanted Luke. He wasn't stunted like Vader was. He had the potential to be far more powerful than Vader.
Vader is a truly tragic character. He turned to the Dark Side due to the promise of power, then he lost it all.
Also, Dooku and/or Palpatine arranged for his mother to be kidnapped and tortured by the sandpeople. Anakin's fall was set up right away from his introduction. The prequels aren't as ham-fisted as people like to make out.
But Jar Jar still sucks.