I like maintaining lore, I think the Human supremacy of the empire is a core concept of theirs, instead of changing you should look into justifying it. trying to change it would change the way you would think.
for the emperor, why don't you use the old idea that he was simply trying to prepare for the arrival of the yuzhang vong, just replace the vong with something you know. not stupid.
that way you can keep the classic emperor and vader which are both great characters in their respective ways, and just twist them ever so slightly. keeping vader as the emperor's enforcer is really fun to play, and his reputation will precede him when/if your players run into him.
I did an imperial based game and I always tend to show the brighter side of the empire, it brings order and stability. as well as change, may not be great for everyone but can do it, unlike the festering republic.
storm troopers are a complete separate military branch, and are selected from the imperial army for more training anyway clones simply aren't as reliable as born and bred humans, couple that with the kaminonan rebellions. and you got a distrust for clones.
you could have the force users fall under the jensarii or the imperial knights, or have them form underground force cults
don't make vader an inquisitor it doesn't fit him.
in fact don't use the inquisition they are stupid in the SW universe, just use ISB and have there be agents who are force users.
in the end keep palps and vader the way they are, to give some grounding for the verse your players are in, you can always make up new grand moffs, or officials who "truly" govern the empire while the emperor does fuck all.