If I was in charge I would do that.
Any more "War for Cybertron" material will just be DLC (downloadable content). Just put out some mini-campaigns set in the broken wasteland of shut-down Cybertron. The players scroung for energy before you starve while taking shots at the Decepticons. Sounds pretty grim, in fact. Has a sort of Terminator/Mad Max feel to it.
But, the big thing is to move straight into sequel territory with Transformers: War for Earth.
The only thing is I would NOT change the controls for the game. I would still allow the cars to strafe sideways and jets to hover. After all, once you start shooting you've blown your cover. Having the car wheels turn 90 degrees in their wheel wells is fine with me (but not default to hover cars). Or just have guns on turrets so you can shoot sideways and always drive forward. Tanks obviously are easy to do this, but cars and planes can have really small turrets.
I would add two other things to the gameplay. I would have most of the human race not automatically accept ANY of the Transformers as friends (some do, like Spike and Sparkplug Witwicky). The good guys have to go back into hiding after they help out, because I think it is more plausible that humans would want to capture all Transformers, disarm them, and then only after a few years let them out. There would be missions where you have to "sneak" and not do anything like strafe sideways as a car or break the speed limit, or hover as a jet. Those will blow your cover and fail the mission.
I would say it would be hard to hide the fact Transformers are here on Earth. The first Transformer walking around in public is going to be on TV in no time flat. You just can't find them later because they can be anywhere or anything. The "Hiding in plain sight" element should be used and justified. That is the whole point of copying human vehicle shapes. If Autobots were allowed to operate in the open, they wouldn't bother with copying human vehicles. Just like Superman or Spiderman, they are heroes with secret identities they need to keep concealed until the day people get used to them and trust them.
The other thing to add is Gestalt characters like Devastator. I would let three players merge up with a few NPC characters to form the "Big Guy". The first player drives the bot and has some offensive power, but the other two guys are the arms making them turret gunners with more firepower. In effect this is the vehicle combat you see in other games like Battlefield 1942 and Bad Company. Multiple players operating one vehicle. The NPC characters are just the unmanned "tank" sitting around waiting for players to use it.