Joanna and Jonathan got married and Jonathan took Joanna's name.Perfect Dark Zero takes place in 2020, and Jonathan's last name is listed as Steinberg, with "Dark" being Joanna's family name. In Perfect Dark, which takes place 3 years later in 2023, Jonathan's last name is Dark. They married during those 3 years and Jonathan took her name...probably because it was much cooler than Steinberg.
Joanna simply completely forgot about the name Dr. Caroll between Zero and Dark.3 years is a long time to try and remember a mostly unremarkable (never mind his accomplishments) somewhat elderly scientist who died during a rescue attempt amidst other scientists who may have died during said rescue attempt. And when Joanna finds out that the Dr. Caroll being held hostage by dataDyne is a floating AI programmed with the personality of that long-dead scientist, and considering the AI is working on roughly the same project the original Dr. Caroll was working on? Gee, hard to believe she doesn't connect the dots.
Joanna Dark was intended as character in SSBM.Evidence is with motion sensor bomb and the cloaking device. I guess when Rare being bought by Microsoft it couldn't be done.
Perfect Dark and the original Goldeneye are set in the same universe.This would explain the guns in the glass cabinets in the firing range.
Following from the above, the License To Kill difficulties in Goldeneye and Perfect Dark can be justified by an arms race.In this difficulty, both the player character and the enemy have zero health, although explosives and autoguns are incapable of instant kills (paradoxically making them less lethal than regular enemies). This came about because NATO and the Soviet Union had a small-arms race in parallel with their real-world nuclear race. In this violent world, it became imperative to kill a combatant before he could end you first. Handguns were given deadly hollow point ammunition which was so effective as to allow an instant-kill even if shot in the hand or foot. Shotguns were loaded with explosive rounds which also guaranteed maximum efficiency. Sniper rifles and various machine guns were similarly customised and only the Klobb couldn't achieve instant kills, but was still as deadly as a real-word assault rifle. Knives were also laced with poison and James Bond had enough martial arts knowledge to kill anyone with a single slap. But the United Nations banned autoguns and other unorthodox weapons from using such ammunition. The Soviet Union were forced to comply with these regulations and the Janus Syndicate couldn't do anything to upgrade the weapons they bought/stole from the former superpower. By 2023, even dataDyne couldn't develop hyperlethal autoguns. However, they decided to use deadly drugs in so-called "tranquilliser guns" which made a mockery of their name. Every soldier started to employ brutal hand-to-hand fighting techniques which could (and would) also kill. And when the Maians and Skedar joined the fray, of course their energy weapons were brought to play with deadly consequences.