(Long, I'm a Transformers nerd)
I haven't watched the new one yet, but will give it a try. I was a huge Transformers fan growing up followed closely by G.I. Joe. Neither went the direction I would have liked with their movies.
The previous Transformer movie along with the new one appears to be telling some of the origin story judging by the previews, but it mixes in the stupid knights storyline and made the Dinobots retarded.
If I made the series, I would have introduced the characters, gave a little backstory, and of course had some major battles in the first movie. I probably wouldn't have killed off any major characters yet.
I think the second movie could have been a good point in introducing some new characters (like maybe the dinobots and constructicons). It could have a storyline about the Transformers needing energon to survive and how the decepticons were going to steal human energy sources and convert them to fill their needs.
I think the third movie would then be a good point to do a live action version of the Transformers (animated) Movie. This is when they start killing off a number of main characters while creating different versions of some of them with the Unicron storyline. Instead of Unicron attacking Cybertron, have him coming after Earth. Disaster movies on Earth tend to do well. They could also introduce the Matrix of Leadership and how it switches hands.
If they did kill off Optimus Prime they can then bring him back in a 4th movie with the Quintessons (the creators of the Transformers). That is if the movies did well and there was a reason to go beyond a trilogy.
Michael Bay just turned it into a mishmash of old and new storylines to the point of it not making much sense. I don't think there needed to be as much changed as they did. Us 40+ year old folks that grew up with the Transformers would have appreciated it more if they kept it more old school I think. The newer younger crowd would have liked it as well still.
They probably will end up rebooting it in about 10 years anyways and will hopefully do a better job.