Omega Supreme is no slacker and even after being hit down, he just stands back up. What to do?
The bigger they are... ;p
I recommend playing as Megatron for his cannons but definitely choose a Decepticon you're comfortable with, because you'll be battling Omega for a while.
Omega Supreme will begin by shooting his various gun turrets at you. There's a total of 8 but you would only need to personally down 4, I think, before the rest explode and Omega searches around for a means of repairs.
Barricade will note the puzzling thing about video games at the sudden appearance of an energon canister for Omega ("Is that supposed to happen?" ;p). But that's your chance to get back at the Supreme machine.
Use the blue marker to help locate and Interact (X) with the canister to poison it with dark energon. Omega Supreme will pull in the canister and be infected, turning purple, and opening himself up to your standard attacks while he focuses on purging his systems. Aim for the head in the small window of time you have and then retreat once Omega Supreme's color returns to normal.
Soundwave will mention the tractor beam Omega Supreme has in one arm. Besides grabbing energon canisters for himself, he will also try to grab you to deliver some major hurt. Don't give him that chance. Hide behind the walls and simply keep moving and jumping ahead when you see the signature red target circle around you. You will notice that he would oftentimes rip away a section of wall in his efforts to reach you. Keep moving.
Energon cubes and ammo are readily available and are reguarly replenished around the area, so don't be afraid.
Do avoid the area around Omega Supreme though. One step by his feet, you're dead. One ground pound shockwave, you're most likely junk. If you're going for the Autobot symbols though, there is one down there at the fountain-like structure behind a shield box, so those may be worth the risk. (Another symbol is on one of the wall sections and will definitely reveal itself when its wall crumbles, I found it lying in that wall section's rubble.)
After this first round, two Aerialbots will divebomb you each time you clear Omega's turrets (to keep you from the energon canister, I suppose). One well-aimed blast from Megatron's cannon will knock each down (see why I like Megs? ;>). And you can continue poisoning those canisters!
Once Omega Supreme falls, he initiates further repairs by opening his chestplate to channel energy from Cybertron's core. This ups the ante by allowing him more powerful cannon strafes that razes everything in their path. And gigantic missile barrages that can home in on you from anywhere. So if you hear missiles, move! And just keep moving!
BUT, this leaves Omega's chestplate open and his insides vulnerable. hehe
As you move, get potshots in every time you face him. This is also a good time to get the Devastator achievement as Omega's cannon blasts apart the pillars as well as the wall, so keep light on your treads and wheels and you should be able to get this chieve in the bag as well.
There will also be consoles that you can activate to setup mounted cannons. But DO NOT be tempted by them! I tried numerous times to make use of them and only came close to killing Omega once. Mostly, Omega Supreme's cannons and missiles would take care of you long before you can do any significant damage. Reason: Slows you down. The animation of manning and leaving the cannon is in real time so you're very vulnerable in-between. And with Omega Supreme's constant attacks, you need to keep mobile. Even if you detach the gun, you'll run too slowly with it to be agile enough to dodge. So stick to your own guns (ha) and keep at it! (Which again is why I chose Megatron, his tank cannon comes in very handy here.)
Once Omega Supreme's insides are cooked, Megatron will infect Omega fully, winning you the battle and the level! Congratulations!