I don't quite understand what the problems were for those who call themselves Transformers fans. It really took alot from almost every continuity to appease any fan. Here's where RotF remained in-continuity with the first 2007 film:
[CAUTION: SPOILERS]
* - Prime's dialogue at the end of the film confirm he transmitted the message to outlying star systems. It can be further acertained that, from the way the narrations are constructed in both films, he is creating a recorded journal of the events of the war and his time on Earth... just as any commanding officer might do in his spare time.
* - Megatron laments in RotF that with the All Spark gone, the power and knowledge needed to further their race (so as to militarize & control them), to which "The Fallen" responds by revealing that the Cube was merely a vessel and the Cube's power and knowledge merely took a new form; the knowledge obviously transferred into Sam, and the power transferred into Megatron. The transfer wasn't complete however (due to two pieces of the All Spark Cube not being able to complete said transfers), as evidenced by the fact that Sam's cyberglyphic knowledge didn't kick in until after he touched & looked at the Cube splint (it's last bit of energy transforming his kitchen appliances and later re-invigorating the dormant Jetfire) and the fact that the Cube Shard fully embued Megatron with enough energy to fully reformat the cannibalized parts from the Hightower drone into his superstructure - creating an all new tertiary form (his tank mode).
* - Sam seeing symbols and acting extremely strange after touching the Shard jives with his great grandfather seeing symbols and acting strange (apart from going blind from the literally blinding energy) after Megatron instantly copied/transferred random information about his race and the Cube to him upon being touched.
* - Scorponok was last seen retreating into the sand wounded and broken. A full two years after the event in Qatar, Scorponok was no doubt alerted about the conflict in Egypt via Soundwave's updates in time enough to critically damage Jetfire before being severely crushed by him. The transformers of the film universe have been confirmed to be able to grow back parts like lizards grow back tails, just as thoroughly as any living organism would heal. This is also shown in the first film when we see that Blackout has grown back the parts to his vehicle mode that Scorponok originally composed.
* - Simmons refers to Sam as 'the case that closed Sector 7'. This makes sense in that Sam's actions in assisting the Autobots (i.e. giving them the glasses, having Bumblebee freed, as well as being the great grandson of the person that blew everything wide open so early) proved that Sector 7's advanced research status was unsuitable for such an inept division of the government. It was shut down because the events two years prior had proven it obsolete.
* - Prime refering to "the Spark in [his] chest" from the first film jives with him not having the Matrix of Leadership in his chest cavity; he didn't even know such an artifact existed. The artifact itself only powered Prime up enough to be physically repaired before being stolen by "The Fallen", Jetfire's Seeker abilities further enhancing him in time to destroy the Harvester and (presumably) the Matrix that powered it.
Items of note:
- It is not known how "The Fallen" escaped his inter-dimensional imprisonment, but he is seen connected to many power cables in his first appearance in the film. Considering the point made about that fact that the Protoforms contained on the Nemisis need more Energon to fully form, perhaps the cables hooked up to "The Fallen" indicate he was funneling portions of his massive amounts of energy to the budding Protoforms.
- Ratchet's Plasma device that was created to aid in the repair of Bumblebee's complex voice box components did not work; not only did Ratchet claim he was "still working on them" two years earlier, but he doesn't seem to confident in his device to begin with, tapping it after he uses it on Bumblebee, as if he wasn't satisfied with it. Still, Bumblebee is "playing it up" for sympathy's sake.
- The Audi automobile chased & destroyed in Shanghai my very well be Barricade; the robot mode is ASTOUNDINGLY similar. It was made clear in official prequel material that NEST simply could not catch him due to his uncanny ability to elude them during his fact-finding missions after the events of the first film. Considering how adept he is at gaining information, he could have travelled to China (perhaps picking up different alternate modes along the way) to aid Demolishor in prepairing for both "The Fallen"'s and Megatron's return; once Demolishor was engaged by the enemy, Barricade fled in order to further the preparations and perhaps warn that the Autobots were getting better at catching & defeating them... until he was utterly destroyed by Sideswipe.
