You've made two key changes:
- Allowing multiple combat half-actions per round
- allowing movement to be replaced by a non-movement half-action
The primary factors I see are:
- increase in Psyker offensive capability (Most of their offense is more powerful than their allowed weapons; it gets worse under RT or DW, due to a different psychic system)
- decreased access to defenses¹
- decreased emphasis on movement²
- increased emphasis on non-action defense (IE, cover)³
- breaks the equipment bonuses
- decreases incentives to use burst and full-auto autofire modes
- cybernetics and talents with extra half-actions become devalued⁴
- initiative becomes more important⁵
- Ganging up becomes less essential⁶
¹: Since one gets very few defenses per turn, this change of yours makes them less valuable, by allowing them to be overwhelmed faster.
²: The current system makes movement a valuable and essentially irreplaceable part of the round; take it or not, it's lost if unused or unusable. It's not terribly realistic, but is very cinematic. And DH, RT, and DW are all intended to be very cinematic in tone.
³: At present, especially for melee, active defenses (dodge and parry) are quite valuable; cover is less so, but not enough to render it useless. When one allows replaceing movement with a second attack, cover suddenly becomes MUCH more attractive, as it's an assured penalty to be hit, instead of a roll by the defender... but it also reduces drama.
⁴: At present, the only way to get a second attack is expensive talents and/or cyberware with inexpensive talents. If a character can just hole up in cover and double shoot, these talents are far less valuable, making the Assassin and Guardsman's additional combat actions less useful.
⁵: Further, by allowing the etra attacks, you can run a target out of actions sooner, as well, so initiative becomes more important to prevent having actions drained in defenses.
⁶: Ganging up is the great equalizer in RT and DH combats; it's how one overwhelms defenses. Given that every character can defend once for free, and once by aborting, if you can attack twice, you've just eaten both defenses this round, meaning you only need one attack from a buddy to get through. The norm is that you need two buddies to negate the defenses, or one buddy with a multiple attack talent.
It sounds like you made these changes with rank 1-2 characters... it's going to be more profoundly off-norm or higher rank characters, as normal slow growth of actions is made to feel even slower by providing far less of a bonus over not having them.
There is not a canonical "D&D" answer. The answer differs per campaign world.
I know it's a little weird - the D&D 3 core books don't present themselves as a generic system per se; they hint at a shared cosmology with the gods, certain roles for the races, etc. that makes it seem like there's a larger world there. But it's just a hollow shell, to be filled in either by yourself or by the specific campaign worlds (Forgotten Realms, Greyhawk, Golarion, etc.).
Now, in 3e/3.5e Greyhawk is the default setting (they didn't follow through on that real well but it was stated) so you could look to the Greyhawk answers as the canonical defaults. I don't know that they ever answered the "but where did they all come from" questions, and I was a Greyhawk aficionado for decades. Canonfire! would be the place to research that. If you're looking for Corellon specifically, try this wiki article. Most campaign worlds are deliberately cagy about how exactly the beginning of all things transpired, however, and Greyhawk is especially so.
Best Answer
They have never been on "Good" Terms
Chaos and the Emperor have always been at-odds, however, what the exact story is tends to vary.
The most generally-accepted origin story, and by that I mean the one most-often referenced by the community and by GW itself, is the story of the Shamans, sourced from Realm of Chaos: Lost and the Damned (1990).
Realm of Chaos: The Lost and the Damned
In this version, the Emperor is the combination of the souls of a group of human Mystics called Shamans. The Shamans guided humanity, but, as the influence of the Warp grew (note that the Chaos Gods themselves were still dormant at this time), they found that they were dying-out, and their reincarnation abilities were beginning to deteriorate due to Warp Predation. Recognizing Mankind's need for guidance, they took poison and "died as one", which allowed their souls to collect and reincarnate all at the same time, and escape the predatory spirits of the Warp.
(p. 174-175)
At first, the Emperor tried to simply "guide" Humanity, manipulating it from behind-the scenes to avoid the paths of Chaos. However, as he did this, the Chaos Gods became more and more aware of his actions and began to wake. Each God opposed the Emperor:
All of these are predicted (but not entirely sourced) to have occurred within the 40K Terra's "Medieval" Period but have extended up until the Unification Wars, the conclusion of which decreased the influence of the Ruinous Powers in humanity by unifying Humans into one purpose: the Great Crusade, after which Horus betrays the Emperor and 40K history is born.
However, it wouldn't be 40K if there wasn't another story that casts doubt on the canonicity of the Shamans...
Vengeful Spirit (2014)
This is the story that you have heard referenced in the comments on the question. In Vengeful Spirit, the Emperor and Alivia Sureka travel to Molech and enter a Gateway to the Realm of Chaos. Here, the Emperor makes a pact with the Chaos Gods where he gets power in return for spreading Chaos worship throughout Humanity, but immediately reneges on his end of the bargain and becomes the Anathema.
Of course, this has some inherent flaws:
Either Way, The Emperor and Chaos have never gotten along