So let me get this right; Megatron, from the first film, wanted the All Spark to transform human technology and take over Earth. That's Sam's and the Autobots assumption from the first film. But, as we learned in the second film, he was actually a Seeker amongst many Seekers working for the Fallen. Megatron was sent to find the All Spark so the Fallen could use it to find the location of the Matrix of Leadership in order to reactivate the Sun Harvester. With it, the Fallen and Megatron could destroy the Earth's Sun, harvest it's energy and rebuild Cybertron. So far so good right? But, Bay and Kruger decide that all of that was bull**** so they devise a plot that says that Megatron was ALSO plotting with Sentinel Prime during the Cyberton War that would use new technology that only Prime can use that would bring Cyberton into Earth's orbit, harvest the Earth's natural resources and then use humans as slaves to rebuild Cybertron. Oh and that bull**** about Optimus Prime being the last of the Primes was also **** because there's actually one more on the Moon. I'm a big Bay apologist but even I can't buy the damn plot to this film. He basically retconned his first two films with this picture.
I think that the story weaves its way around the other films pretty well. TF2 is a cinematic turd that needs to be expunged from the record so ignoring it is a good thing, and TF3 wisely glosses over it, telling us that Megatron came to Earth (and subsequently crash-landed in the Artic or wherever, setting up the first film) in order to meet Sentinel Prime and get their plan underway. SP was lying dormant and could only be revived by another Prime, so the Decepticons stashed the canisters. They found out that the Allspark was on Earth (quite a co-inkydink, eh?) so they went after that first, which led to Optimus Prime and the rest of the Autobots showing up in TF1. With Optimus on the scene, the plan with SP could then be put into action. I loved the twist with SP, as it showed that there's more than just good and evil out there. He's doing what he's doing for the 'greater good'.