Without having read most of the thread, just a few things that are in my head-canon:
1) WW3 wasn't a nuclear war between nations. It was more akin to a worlwide civil war, where nations crumbled, and militaristic/religious/xenophobic terrorist groups fought against gouvernements and each other, resulting in a worldwide period of chaos and failed states. Nuclear warheads were exploded, but not against other nuclear armed nations but against "terrorists", and a lot of radiation came from reactor catastrophes from unfunded and unmaintained nuclear power plants. Basically: More "Mad Max", less "The day after". The "Eastern coalition" mentioned in "First Contact" was a radical hacker group that gained control of satellite systems and targeted them against their "enemies".
2). Zephrane Chochraine wasn't a drunk hobo that stumbled upn a warp drive. He was one of the most prestigous scientist in the world, with his own institute, that was refitting the Phoenix way before WW3 started. But when gouvernement fell, cities delved into chaos, he turned into a bitter alcoholic. He and his scientists stayed and continued working, but were bogged down without funding and the need to self-supply during the chaos.
3) Khan and his fellows were the result of genetic engineering, not selective breeding. Also, the Eugenic War wasn't fought in 1996, but much later. In fact it was the same "dark time" usually mentioned by Q, with the same mock-trials. The characters simply misremembered the dates, the same way many people today think WWI (1914-1918) was fought against Nazis.
4).The "Earth-Romulus" war was entirely fought in Federation space - by Romulan drones against Earth ships. Much like the USA is droning Pakistan and Afghanistan today, Romulan tried to disupt the Earth Alliance with drone attacks. That's why nobody ever saw a Romulan - they only fought their technology. It ended, when the Romulan drone program was shut down after much escalating and use of nuclear weapons. Earth propaganda immediately turned that into a "victory". A treaty was signed (with Romulan signature in absence) to make the use of weaponized drone ships illegal - that's why we never saw Romulan drones like in ENT later in the future in TOS or TNG. Only a few hundred years later, with the economic powers of many different races combined, the Federation suddenly became equally powerfull as the Romulans. Basically, for Earth it was their "Independence war". For the Romulans, it was Vietnam.
5.) The Enterprise from ENT was referenced in history books only as "NX-01", and the history of Archer's exploration mission was overshadowed by the Romulan war, that's why the NX never was included in the starship gallerys of later "Enterprises".
6.) Most of the "human aliens" on TOS, or the "forehead-ridges" aliens on TNG in reality looked truly alien. They were just too alien for us (present day viewers) to read their emotions, while future-humans were trained to do so (much like babys can read the emotions of monkeys - but loose that capability because it isn't useful for them in daily life, they learn to read alien' faces, but keep that ability). It was just "made easier" for us viewers, so they were portrayed as mostly humans. In reality those looked like reptile or starfish aliens though.
7.) The fleet sizes of the Dominion war were much smaller than implied. When they say "we lost 100 ships", that means only a handfull of supersized ships like Galaxy class or Nebula class ships. The majority were always much smaller ships, the size of Nova-class, the Raven, "Insurrection"'s scout ship or only runabouts. Also, all ships had their shields active, and it took much longer to destroy some ships than seen on screen. Also, the Enterprise-E, Intrepid- and Nova-type ships all took major parts in the battles.
8.) There are more types of Borg drones than were seen on screen. There are repair-drones, combat-drones, exploration-drones, medizine-drones, and leader drones (like the queen). All are part and voice of the greater collective though. Even the queens. But much of the tactical thinking of the hive-mind "voices" itself through the queens. Also, the Borg don't care much about humanoid bodies - that's why they don't clone or breed their own armies like the Dominion. They care about assimilating "experience" and knowledge, that's why they are always hunting other sentient beings, instead of "farming" mindless drones. They are more interested in assimilating beings that fought against them and developed new tactics and technologies, than completely wiping out other civilisations - that's why much of the Delta quadrant can survive on a low technology-level, and why they always attack Earth with only one ship.
9) Romulus wasn't destroyed in the prime timeline. The Narada, red matter, future-Spock, the Jellyfish and the Hobus supernova are all part of the original future of the JJ-timeline. Which always was a parallel timeline. When Spock and Nero travelled back in time, they only changed the future of their timeline, not the prime-timeline. In the Kelvin-timeline, Khan was always white, starships had front-windows instead of viewscreens, Sarek was played by Ben Cross, and the Franklin the first warp 4 ship. The original Kelvin-future was much closer in looks to the prime universe than after Nero's incursion though.
10) In the Star Trek universe, there was no "Star Trek" tv-series in the past. Instead they had a popular space opera called "Galaxy Quest" on television. Whose actors once were abducted by real aliens...
