I wonder if the producers ever look at this site...They might get some ideas! XD
Ah well, just in case, I'll post mine:
Extend both Jolt and Ratchet's roles - They had so little screen time. Jolt needs some lines, as well. Give him some good lines and develop his character. (Ratchet was even more underused in #2! As if his role was short enough in #1!)
Sideswipe - One word; MORE!
Give Soundwave a decent amount of action - As awesome as he was, he was missing out on the action, below! (I bet he was seething.) And bring him to Earth, too.
Unicron - Enough said.
The basic story could be that the Decepticons are really pissed because of their second defeat. As it happens, Unicron is approaching; Megatron makes a deal with Unicron and Soundwave tells Unicron of the humans' dependence on everything electronic. Soundwave then disables everything on Earth (as his toy bio suggests) and bring the continents to a standstill; global disruption (think 'Live Free or Die Hard', but bigger), so that Unicron can make an easy meal of Earth. The only thing standing in their way is a dedicated team of Autobots, as they try to get everything back up and running (thus, Jolt's role can be enlarged, instantly).
And then you have a basic underlying structure which would be centred around 'opposites':
Introduce Prowl - in his police car, he'd be a match for Barricade and it'd clear up Barricade's role.
Introduce Nemesis Prime - Optimus' evil twin and stick him in a Kenworth Truck; I have a photo of a sweet Kenworth cab and it looks so deliciously evil. Perfect match for Optimus.
Soundwave's Earth form - Possibly an F-35; basically an F-22 that hovers (if you know your Lockheed Martins), so he'd be a direct negative to Starscream (seeing as how Starscream is very deceptive behind Megatron's back and Soundwave is one of his most loyal soldiers).
Also, Soundwave could have his voice damaged and his vocal processors crudely repaired, making him sound more like his G1 counterpart...
Take 'em or lave 'em!