Stupidity: The Analyst wishes to hide the true identity of Neo from anyone inside the Matrix, so his appearance is altered. But in this new Matrix Neo is also named Thomas Anderson, his name from before he was pulled from the Matrix originally, and he is a famous game developer that created a video game series called "The Matrix." It is frankly astounding that anyone actively looking for Thomas Anderson would not immediately see through this ruse and instead would be fooled by balding hair.
Plot hole: Considering how important it is to the Analyst that Neo stay connected to the Matrix at all times, it is unfathomable that his body in the real world is unguarded. While keeping an eye on him inside the Matrix at all times is difficult, there is no reason whatsoever that he should be left alone inside his pod with no security for even a second. This is an entirely different scenario than the original 3 films where resistance fighters finding Neo was integral to the machine's plans.
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