As a result you have prosecutors doing what they do best, throwing everything at the wall and seeing what sticks. The problem with throwing everything at the wall is that defendants are more inclined to accept a reasonable plea rather than face the unknown.
For example, is it reasonable to charge someone with a count under CFAA for each instance they try to access a system without permission? You can try to adapt existing case law in unrelated crimes - such as attempted murder, should someone be charged for a new count of attempted murder for each bullet that was shot at a given victim or just a single count notwithstanding the number of shots fired, or how about if there are 2 potential victims the defendant wanted dead but only shot 1 bullet near both of them? Is it reasonable to charge a count under CFAA for running vulnerability software on a website? Is it reasonable to charge someone for breaking and entering if the defendant simply checks to see if doors or windows are unlocked, should we file an additional count for each door/window that was checked or a new count for each time a door knob was turned?
These are all issues that are ripe for the courts to decide, but it will take a very long time before you have a defendant willing to take the risk. What is really troublesome is that in the meantime there are cases such as this where 44 felony counts can be reduced to a single misdemeanor in exchange for a change of plea. The fact that a prosecutor was willing to offer a deal like this means the original charges were improper even in the eyes of the prosecutor.
Expect things to only get worse in terms of prosecutorial discretion vis-a-vis charges under CFAA in the foreseeable future.