Plot hole: Although William Lewis burns his fingertips in an attempt to avoid identification, the Special Victims Unit could have identified him early on by examining the remaining unburned area of Lewis' hands, and in good police procedure still record the newly scarred fingerprints, as these new scars actually make his fingerprints more unique. His scarred fingerprints would still be at Alice's apartment crime scene, and during the trial at the end of the episode the prosecution would still have a strong argument for placing Lewis at Alice's apartment, even if the DNA evidence is thrown out because of alleged cross contamination.
Plot hole: M.E. Warner explains of Lewis and Benson "both their fingerprints are on the gun." Lewis burned his off in a particularly gruesome scene a few episodes earlier. (It was at the beginning of his arc). Only Benson's should be on her gun. (00:29:20)
Answer: I didn't see the show so I don't know the details. A general answer would be because a reckless endangerment charge is easier to prove "beyond a Reasonable Doubt" in court and get a conviction. This charge would not require the prosecutor to prove intent, which would be required for proving aggravated or simple assault. Also, if there were no visible injuries, it is difficult to show bodily injury. Just because the reckless endangerment charge was specifically mentioned, it does not necessarily mean there were not other charges filed. Police often make multiple charges, like lesser-included offenses, so that the defendant's act will fall under one of them if the legal requirements are not met for the others, if they are not sure of the best charge to make (the district attorney knows and can decide), or to have something to plea bargain with.
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