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So this is something I have been thinking about for a very long time now...I've come to see the Imperium of man to be corrupt in its higher ups like the High lords of Terra. Now as this is all just speculation I want to get your guys thoughts on this. What I see is that everything the Imperium is now is just what the High lords of Terra and the Inquisition want it to be not the way the Emperor would have ruled it. Do you guys think there actually following the Emperors will or is that just what they want everyone to believe? As I see it the true enemy of the Emperor is the Imperium its self as even the Inquisition stopped one of there own founders and his generation of followers from trying to revive the Emperor. Id love to get some ideas on this as its hard for me to determine who is really good and as I told my brother if I ever get into 40k again and actually have the money for it my Space Marines would be reneged from the Imperium but not chaos.
(If you can't tell I really REALLY dislike the inquisition)

Yes, you are right.
The Emperor would be horryfied if he saw the Imperium in it's current state.

Maybe it's the reason why he refure to come back from the dead. He would suffer instant hearth attack. *You should laugh now. Remember the Inquisition*

The problem, I think, is that the High Lords, are doing the best they can.

I mean, the inquisition is necessary because Chaos is so pervasive, and I can't think really of how to change the system without having it come crashing down!

Blame Lorgar and his lectio divinatus (idk how to spell it) that got people believing that he is a god. And that belief took root and a very strong hold on every one. If the Emperor came back he would have so many beat downs to administer.

The Sad part is he's probably aware of it, if the Emperor's Tarot is any indication. Plus, it's not like they have any alternatives, since this is one setting where the wrong faith can actually be deadly.

The Horus Heresy novels are starting to hint that the whole thing was foreseen to a degree by the Big E and he is playing a chess game against the chaos gods to tweak the outcome just enough to give man kind a chance. The Imperium is messed up but it's doing the best it can given how messed up the universe is.

(If you can't tell I really REALLY dislike the inquisition)

To fear the Inquisition is redundant. To hate them, heretical.

The Inquisition is doing exactly what the Emperor told them to do. They do whatever is necessary to defend the Imperium.

If you want to know who really fethed up the Imperium? The Space Marines. Specifically, the Traitors, and all of those Chapters that went renegade in the following millennia.

Burning a tainted world and being paranoid of everything is necessary with an enemy that can appear from nowhere and spread like cancer. The inquisition needs to be unreasonably extreme because it's the only reason course of action given their options. Sure they often go "to far" but going to far is better than not going far enough when dealing with something as dangerous as chaos. It's safer to kill someone who "could" be guilty than to only kill if proven guilty, as the price for pardoning a corrupted person is so high that it could literally make billions of people fall to chaos.

They are being the lesser of two evils, and being the bad guy as its a necessity if they wish to do good. The fact that the inquisition could almost be admirable is truly both grim, and dark.

To go a bit further:

As I see it the true enemy of the Emperor is the Imperium its self as even the Inquisition stopped one of there own founders and his generation of followers from trying to revive the Emperor

The operative word here was "try". They had no guarantee of success, and no way to know what would happen if they allowed the Emperor to die completely (they still don't, all the "Star Child" theories are fan speculation). This event you're referring to is the sort of situation where you're betting everyone and everything, the fate of the entire race of Mankind, on the slim chance that you can resurrect the Emperor.

Of course they didn't go for it, it's a foolish gamble. They had an extremely remote chance of success, any other result would be the doom of all Mankind. So of course they didn't do that.

They get a lot of crap but they pretty much have one of the worst jobs in the world. They spent their whole lives investigating dangerous corrupt and evil people, with the best case scenario is you die a good death. worst case you become the thing you were trying to fight.