These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Badass Decay: Lustbader changes Bourne from an unstoppable juggernaut into a whining wimp who wouldn't win without outside help. See Flanderization on the Literature page.
Creator's Pet: Lustbader's Arkadin in the books. Lustbader keeps filling the narration with Arkadin's past and making Bourne exhausted so Bourne cannot kill Arkadin. When someone writes Bourne novels and guarantees upfront that the villain is going to have his own trilogy, you know that villain is a pet.
Designated Hero: Arkadin, in the flashbacks of his past. The narration is meant to make readers sympathize with him, his tormented life in Nizhny Tagil, and his struggle against various Russian crime bosses. The problem is that, even considering all that, he is still a murderer, a terrorist, in a life of crime for selfish gains, and no better than any other Russian gangsters he kills.
Designated Hero: Aaron Cross is really just an innocent man trying to survive, but demonstrates himself to be a fair bit more ruthless than Bourne is in trying to do that. In particular, he seemingly kills a couple of security guards at the Manila factory, damages a lot of their equipment for a distraction, and knocks out the plant manager for no other reason than to steal his watch.
Cross and Shearing are extremely popular in fanfiction.
Popular Australian Actor/Comedian Shane Jacobson's brief appearance as the Factory Owner in Legacy was well recieved by Aussies, many of whom paid more attention to him in his scenes than anyone actually relevant to the plot.
Harsher in Hindsight: In the beginning of Ultimatum, Bourne revealing insider information about a top secret and sinister program run by an US government agency to a journalist working for The Guardian is bearing an eery resemblance to what Edward Snowden did six years after the movie's release.
Herr Doktor: It's so subtle it may very well be just coincidental (he has no accent and no information on his background is given), but Albert Hirsch does at the very least have a German name.
Iron Woobie: Let's just say Bourne had a lot to go through.
Just Here for Godzilla: Many Filipinos, especially Manileņos, turned out to watch Legacy mostly because the last half takes place in Metro Manila.
My Real Daddy / Only The Creator Does It Right: One may argue that the Bourne series has two daddies with Doug Liman and Paul Greengrass. With The Bourne Identity, director Doug Liman gave the film a unique style, but it was Paul Greengrass who would flesh it out in its sequels The Bourne Supremacy and The Bourne Ultimatum, with Liman still involved as executive producer, garnering even greater acclaim. But when Greengrass turned down the offer to direct The Bourne Legacy, Matt Damon left with him, saying he wouldn't do any more movies without him, and Liman left too. This is part of why Legacy hasn't been as well-received as its predecessors.
It should be noted that Tony Gilroy wrote all four films (and directed Legacy).
Nightmare Fuel: In and out of universe. After Marta witnesses her colleague shoot everyone in her workroom, the CIA sent a team of therapists to see if she's got PTSD. One of them holds her, while another forces her gun on her hand and presses it down to her head so it would look like she shoots herself. The worst part? They almost get away with it.
Rewatch Bonus: In The Bourne Supremacy, Bourne arrives in Berlin, he sees a nearby poster advertising the protest at Alexanderplatz, so he'd already been planning his confrontation with Landy and the CIA.
A notable aversion that is somewhere between this and Surprisingly Improved Sequel. Each film is considered to be quite good and at the least on par with each other. Although there are a group of people who consider the third film the best due to having the highest HSQ.
Though some considered Supremacy to be a bit of a step down, with more of an action emphasis and an overload of Jitter Cam (thankfully toned down in Ultimatum).
Legacy is a bit more divisive in this respect, with its very existence of trying to make the series a franchise and reverting what should have wrapped up the series in Ultimatum. That said, the movie was much better received than comparable attempts due to having a few shared members of the production (the same writer, who also takes on director duties) and a great cast with Renner, Weisz and Norton.
They Wasted a Perfectly Good Plot: Several critics felt that Aaron Cross's dependence on constant medication to maintain his high intelligence and fear of losing it were one of his most interesting characteristics, and that it was disingenuous when the enhancement is made permanent.