I am sorry I'm late in this topic. I read it all and here's what I think.
1) The destruction of the Empire:
Aliens? - Big acid bugs.
Silent death? - Violence sensitive bugs.
Starship Trooper? - Bugs.
Genestealers? - Bugs imitating Aliens.
Independence Day - Stupid Bugs with overwhelming tech.
There is a lot of bug threat in Sci-Fi fiction and Sci-fi games.
Why not something more intense?
The Dukes of the Marshes infiltrate during hundreds of years the Secret Imperial Police. Take down the Emperor and take over the Empire for themselves. What they don't know is that they are being used by powerful creatures from the unknowed space. The Shadow Leeches. Terrible creatures that enslave all the sencient creatures they encounter. But the empire was too powerful for a direct attack. For centuries they conspired, used, killed, to destroy the Empire. Attacking key Intelligence positions fragilized the Empire and it crumbled. Now it is ripe for attack.
2) The Name of the Empire
I think that the Empire, before becoming "The Empire", had a name. Probably the name of the species or the planet from which emerged. It can be called simply the Empire or it can have a proud name like "The Kashari", "The Garini Archipelago", "The Summit", "The Arm", "Shamar United", "Barnar Unification".
3) Religions and Belief
There is no dark between the stars that doesn't appeal to the gods. What makes the original trilogy of Starwars great is the force and the archetypes. The diferent belief systems in Star Trek. And so on.
And some tech will be "like" divine to some species and it is not necessary to explain it. Maybe telepathy is used to interstellar communication. Everybody uses the skill from the Garazenii, a species that can use telepathy to enable comms to work in instant time from star system to near star system, but nobody knows how they do it and it is revered as blessed.
4) The contenders
a) The Emperor in Exile (I liked Dan's idea)
b) The Dukes of the Marshes (As I stated above. Not many, but with a strong and elite military)
c) The Mechanical Regiments (A well guarded secret of the Empire. All the elite troops of the empire that died or were wounded beyond slavation were introduced in a mechanoid body. Along the years, the mechanoid become aware. When the Empire colapsed, the Regiments moved to restore it. And at the head of the regiments is a man that claims working for the emperor.
d) The United Systems (as the Dan's idea)
e) The Pirate Kingdoms (ragtag of former imperial systems that united in a low tech low law brotherood. The leeches control them.
f) The Leeches (Cold, powerful and deadly. They are coming)
5) The Stage
a) The Empire falls.
b) The Emperor clashes against the Dukes of the Marshes.
c) The United Systems and the Mechanical Regiments fight over territory.
d) The borders start to clear in a new galactic map.
e) The Leeches launch their first attack.