So far, this is the only deleted footage found for the movie:
Sadly it isn't anything exciting and just shows some Autobots gathered around Optimus Prime. The robot running towards Optimus seems to be coloured like Windcharger, which is odd because he'd died in the battle.
There were a few storyboarded scenes which, if put into the movie, would have made the battle of Autobot City longer. Most of these storyboards are from Wombatking.com, which has even more of them here.
Autobots Vs. Devastator
Somewhere between Megatron saying "their defences are broken, let the slaughter begin!" and Prime appearing to challenge Megatron there was a scene storyboarded showing Ultra Magnus lead a few Autobots into battle against Devastator, who had entered Autobot City. This scene would have also contained the only time we see Ultra Magnus do anything in the battle.
Just after Megatron says the line mentioned above, Devastator is shown ripping open a door. This seems to be where these storyboards start, as Devastator enters the city. He doesn't get very far in though as Ultra Magnus appears with Tracks, Sideswipe and Red Alert.
The Autobots all transform and do what any Autobot would against such a large foe: blast it with missiles. Devastator is broken apart, but...
...the Constructicons are all still alive and open fire on their attackers, who are forced to run off deeper into the city.
Sadly Red Alert doesn't make it and gets shot in the back, and is presumably killed (although a storyboard for the Prime vs. Megatron fight shows that he managed to climb out into the open, so he may have survived, or simply died then). As the Constructicons charge in Megatron watches. In the movie itself, Megatron is, at one point, watching and smiling just before Prime challenges him from behind - Megatron was, of course, watching the above scene that never made it into the film. Personally, I'm surprised Sideswipe wasn't the one to get killed off here as he was a season 1 character.
Whilst he doesn't appear in the movie, Mirage did originally have a scene storyboarded.
Mirage sees Bombshell, who doesn't see him.
So Mirage shoots him as the corridor he's in retracts.
But then Megatron shoots that corridor. Whilst it isn't specified whether or not Mirage was killed, but given how he was a season 1 character, it's likely.
Wheeljack was not suppose to die in the movie. In the storyboards for the part where his body is shown...
...the storyboard just has Windcharger and "another Autobot". This other Autobot looks like Smokescreen, who was a season 2 character. Maybe this was changed because Wheeljack was an older character.
Trailbreaker - an Autobot introduced in the first season of Transformers - was meant to die in the movie.
An additional shot of the Decepticons running towards Astrotrain would have shown us the body of Trailbreaker in the foreground. How he was killed is never revealed but this would have been the end of the road for him.
As said above, Wheeljack was almost definitely meant to survive the movie.
When Megatron says "Their defences are broken, let the slaughter begin!" there was suppose to be a pan where we'd see Wheeljack, Blaster and some other Autobots and then Megatron and the Decepticons.
Later on, when the Dinobots smash Devastator through a wall, there was going to be a shot showing Devastator crash through the wall and Bluestreak and Wheeljack moving out of the way.