Hmm the universe vs. universe thingy again. It is pointless to actually talk about such things, but the Covenant and the Empire have more in common than Shivans, plus people will debate this **** anyway for the sake of it. Covenant has plasma weapons, Empire has lasers on an extremely destructive level, both have electro dynamic shielding, both have super-luminal modes of travel to get them anywhere they need in a galaxy very fast that doesn't require jump nodes.
With all of these commonalities why not debate it. After that like the covenant, the empire also has specialized troops for snow, jungle, flying ships, operating other war machines.
When it comes to land attack, the empire has much better land vehicles. I don't really recall anything the covenant had for land assault besides a ship in orbit to really compare to the size of anything in the empires AT vehicles.
Then there comes plasma weapons that the covenant has. Would plasma weaponry overwhelm the empire?
Maybe and maybe not, the lasers in star wars are depicted as very destructive, reliable, and just plain damn powerful. The covenants plasma weapons are depicted in pretty much a similar sense (except for destroying planets..for the moment i think this can be let go).
Then there's the covenants plasma blades, very equal in performance to a lightsaber (does everyone have to rip ideas from star wars to make a new sci fi universe).
The empires dark jedi have a mastery of the much more powerful side of the force. Likely said, Darth vader i don't think could be countered by anything the covenant had to offer, not to mention all of the other powerful dark jedi and sith that exist within the empire. After that is storm troopers. Storm troopers are effective, they work anywhere, and they work great, but they were mainly developed as a measure of superiority over droids and meant to counter droids. After that storm troopers remain a good universal army to protect or counter anything, but the clones usually go into battle seeking and following orders only (that's all they were meant to do really...like i said they clones are superior to droids and were a great way to counter them in the clone wars). Pretty much what is superior to a clone soldier is a battle hardened actual individual, that is what the covenant has over storm troopers.
Another thing to consider is storm trooper effectiveness. Storm troopers are very powerful when recieving orders from someone who has a mastery in the force. Storm troopers get even more effective when you have a jedi or dark jedi fighting beside them. If you integrated force masterers into the storm trooper population per every so amount of storm troopers that would be great.
The covenant still has armies of battle hardened or at least eager to fight troops with a wrath, after that covenant troops do come equipped with personal shielding or at least a shield of some kind, storm troopers just have armor that can be pierced with a laser blast. Another thing is i don't really see a covenant hand held plasma blaster being anymore powerful than a storm trooper blaster. Covenant have sticky grenades which would have an interesting advantage, but empire has grenades also (those thermal ones) which aren't sticky, but still a ballistics quality to the empire anyway.
Another thing is that the empire can keep pumping out clones like nothing. The covenant has tons and tons of troops itself, but those troops aren't clones, they are troops enough to at least be able to think for themselves, and then something in the works of a civil war could happen because someone had a difference of opinion or believed in something else.
The empire on the other hand wouldn't suffer that with storm troopers, storm troopers die, mass clone more of them is what that means, and as many as you wish.
Maybe the empire could possibly annoy, or even make the covenant get tired after a bit storm troopers, that's if the empire had ridiculous nonstop stormtrooper onslaughts. Then again, the covenant has enough of an edge to overtake in swift speed.
There's really only two aspects that make the empire better, which is all of their war machines(things from land vehicles to all of the different varieties of ties to the deathstar) and dark jedi/sith(covenant couldn't overpower the force).
With all of this review, i would say that the empire is technologically superior, but given the ineffectiveness of storm troopers (besides overwhelming an enemy) i'd say the empire better start training more dark jedi, use scare tactics with the death star, and somehow make storm troopers better.