Transformers was awesome, but mostly for scale and intricacy. The story and action could all be improved significantly, honestly.
For the Action, having more clearly defined weaponsets and clearer action with more intricate "special moves" perhaps even borrowing from popular action movies. Seeing the standard duck and cover action movies is so much cooler when you have giant robots doing it. Topping the robot on robot action, honestly, is easy... they haven't even scratched the surface of what can be done with the environment thrown in. Throwing cars? Swining telephone poles? Childs play. Where's the hopping from building to building, using livewires as whips and ripping up parts of the sewer? When do we take turrets from real tanks and fire them at attackers as though they were our guns? The action has PLENTY of room to grow.
As far as story, I agree... the bonds between and with the transformers were... light. There was little brotherhood betweenthem for all the throwing around of the word "brother," and improving those bonds can only improve the storyline. Especially when the integrate the Transformers mythos more deeply into the plot. The Ark and the Matrix of Leadership, for instance, could be awesome, and can play key parts in the film, as opposed to the war on Cybertron which has little significance in the Witwicky Saga... hardly even necessary for the 'origin' of the Transformers.