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Why hasn't he restarted the Primarch program, i.e. made new, better primarchs?
Why hasn't he flat out taken control of the high lords and done away with their treacherous scheming?
Why hasn't he used his influence in the higher echelons of wars to win entire crusades simply by directing them with his will?

I really don't understand or appreciate the new lore that is surrounding the Big E, and his ability to basically make Puppet Saints (Dawn of book series), he can control Battle Sister Cannonesses through observed miracles, and Puppet a Primarch.

I just feel like GW has written themselves into a rather stupid hole here logically. Either the Emperor is All Powerful and capricious/morally divergent, or the Emperor is just a vain god (Zeus) that only exists to further it's own desires and plans, and doesn't actually care.

And I get it, the Emperor is, was, and always will be kind of a jerk by most standards, but then why show him taking a direct stance against Mortarion's and the Warps plans? Why show him doing what he did in the Sabbat Crusade? Why give the power of miracles to the Sisters? It's just so self-contradictory as to the point of silliness.

Because He can't do that.
He can empower Living Saints with a fraction of His power and only recently has He seemingly been able to partially manifest in a sort of host body during the Plague Wars.
For all intents and purposes prior to the opening of the Rift and the Psychic Awakening, the Emperor was dead.
Oh yeah, the Dawn of War books were also written by a guy who didn't understand even the basics of 40k background. He had kids with rocks destroy an Aeldari tank.

Prior to the Rift, the portrayals of the Emperor's actions was more subtle compared to post-Rift and were more along the lines of odd inexplicable events. For example, in the novel Shadow Point, the seeming intervention of the Emperor was the antagonist being critically distracted at a key moment by shots fired at them by a Commissar. After the fight is over, the survivors conclude the character's description of the Commissar intervening was impossible as they found the body of the Commissar...who had been mortally wounded and who must have died before the fight.

Post-Rift we get things like glowing Living Saints with auras of light blasting away daemons. I kinda admit I preferred it more subtle, which leaves more room for nonbelievers like Guilliman to doubt and argue against the claim of the Emperor being divine. It's also more a test of faith if it is not reliably guaranteed to produce results such as making the foe burst into flames.

My headcanon rationale is that pre-Rift, the barrier between the warp and realspace was stronger so it was more costly to intervene in a showy display and the Emperor was weaker than the Big Four Chaos gods and/or husbanding strength for the future. The Emperor therefore intervened in a less costly more subtle fashion, nudging events here and there all across the galaxy. After the Rift, the warp is spilling out into realspace across a vast swathe of the galaxy. It's said that all psykers find themselves with heightened powers, and even those not previously considered psychic started manifesting powers. That points to the barrier between the warp and realspace weakening. That combined with perhaps a new outpouring of faith in the Emperor in such desperate times, has meant the Emperor can afford to intervene in a more blatant fashion.

Well, I mean as close as we can come to canon definition of divinity is unfortunately in the same book, where the farseer define a god as anything with sufficient enough faith to have some noticeable affect on the tides of the warp, which would not only be the Emperor, but would be Gman, and the Saints. This is further evidenced by Emperor's new "abilities". The whole "cauldron" thing.

Setting out specifically what the Emperor can and cant do would require all the BL authors to follow a coherent set of canon rules, which GW specifically doesn't do.

40k is entirely about what sounds cool at the time, and the authors can freely use this ability to write themselves out of inconvenient barriers in the plot.

In my view better not to try to understand it all, and just enjoy the bits you enjoy.