You forgot to mention the part were we lost nine, yes nine Dark Council members in the space of a few years. I'm talking Darth Thanaton, Acharon, Jadus, Vengean, Baras, Arho, Decimus, Hadra, and Karrid. And that's not counting whatever happened to Zhorrid and Baras' sister. Oh and you may as well add Malgus and Serevin to the pile to, who were as good as - oh and why not throw Gravus and Lachris in there too. Its not fair!
Coming from someone with 8 Imperial 50s, all LS V, you couldn't speak to a more loyal and patriotic Imperial :P
So I know just how badly the current situation sucks. And with the new lead writer being the writer who did the JK story (very mediocre at best) it's not looking hopeful for us.
However, it is all explained. (I have 2 republic toons I'm leveling, a JK at 43 and a JC at 30).
OBVIOUSLY SPOILERS BELOW, READ AT PERIL
Due to massive Imperial disorganisation, huge amounts of petty and stupid Sith in-fighting, the Star Cabal & Republic determination to wipe the Empire out, we don't really stand a chance. As Darth Marr says himself during the opening convo on Makeb, he says to my Warrior and my Inquisitor that if the Sith (predominantly -us- being the most powerful and/or influential sith in the empire) don't start working together in solidarity, honour and patriotism we are doomed. The Sith (majority of them) care about nothing else but power, and themselves. They are a blight on the name of sith and should be exterminated (thanks Bane).
Anyway, I ramble.
Empire wins Balmorra, a HUGE bonus for us. But short-lived. The Republic soon takes it back, gaining them and losing us some of the most powerful droid & weapon factories in galaxy. And we also lose Corellia (a small victory to begin with, seeing as it cost us 1/10 of our entire force, a ridiculously huge loss)- did you not play the Black Hole (Corellia bonus series) daily zone? It's kind of the point of it. We lost Corellia, and in a last-ditch effort before we retreat the planet, a small strike team are sent there (with you leading them) to destroy all infrastructure on Corellia, making it a barren, empty, worthless planet which is a drain on the Republic instead of a gain. (also being the founding planet OF the Republic its a moral loss). However, it's still a loss for us.
And as you said, Malgus' betrayal, the loss of another huge swathe of our Fleet (if Empire cannon really is DS, which is lame, then in FE flashpoint the DS option to kill Arkus costs us our fleet, again. Whereas LS saves it...)
And the Dread Masters, like republic getting a destroyed Corellia, its a huge morale loss for us. Dread Masters were one of most powerful weapons we had, and they just buggered off, and are attacking us. YAY!
Also, as is announced on Makeb (whether it's true or not), the Republic formally announces the Emperor's 'death'. a MASSIVE win for the Republic (symbolic win if nothing else).
The Bounty Hunter kills the Republic's Supreme Chancellor. Seems like a win for us, however all that does is bring in the new chick into power, and she is MUCH better, more efficient and war-mongering than her predecessor. All this does is make the Republic sharpen its teeth and claws.
As for Ilum, not a huge loss for Republic. By that time, Jaeric is old and worn-out.
Let's not forget (but connected to Dread Guards) EC- lots of Imperial troops defect and are killed, by us.
Then of course comes the Star Cabal (Imperial Agent story). a massive secret organisation who plays the Galaxy to their own needs. They puppeted the entire war, and play Republic and Empire for fools. They cause the disbanding of Imperial Intelligence - this is ultimately one of the biggest losses the Empire suffers. Imperial Intelligence is the number 1 advantage the Empire has over the Republic. Intelligence is an absolutely superb ministry of spies and assassins, and this is proven that once it is disbanded, the Republic SIS and army gains their biggest victories against us, and we have NO idea what is going or or how to stop it. The Empire crumbles without Intelligence.
Sure there's loads more, but I'm too eager to start playing, so I'm gonna stop writing :P
EDIT- how could I forget about Class stories? lol
Anyway: All Imperial class story final bosses (except Bounty Hunter, but explained above ^) are Sith.. it's *********** ridiculous. All Republic final bosses, are Sith. It's just SO not fair.
Sith Warrior- kills Darth Baras, genius behind the Sacking of Coruscant and the instigator of the Second Great Galactic War (the one we're in now). Ultimately, a pretty big loss... Baras being one of the cleverest Sith around.
Sith Inquisitor- kills Darth Thanaton, another loss for the Empire. Another clever and powerful Sith, traditional, honourable. The reason for his death is also pretty lame, he made a terrible arch-enemy. pointless
Imperial Agent- Act 1- Kills Darth Jadus (for fair reason, but its still an insanely powerful, clever, and logical Sith) and well, Hunter and the Star Cabal, fair enough. but still not anti-Republic. So.. for ALL of our classes, not once of us makes any big impact on the Republic.
However, the Republic is the exact opposite. All we (majority of crappy sith) care about is killing each other, all the Republic cares about is killing us.