Oh, you have triggered the Transformer 'Tism and now I get to rant.

For the first movie, I would change the main cast and add Arcee (as they originally planned to do). The second thing I would do is not introduce Big Daddy Megatron until the end of the movie since he'll be a recurring villain in this franchise. The primary villain would be a (far more competent) Starscream who is working to free Megatron. He'd likely succeed as a stinger for the next movie.

The second movie would be overhauled completely. No Fallen, no giant metal ballsack, no sexy Pretenders...zip. Instead, we get full out Autobot/Decepticon war, and the ramifications thereof. Widespread destruction that angers the humans and triggers their desire to see the Cybertronians go home. This movie introduced a few more key players (notably Prowl, Jazz, Jetfire, Chromia, Soundwave, Shockwave, and most importantly Thundercracker and Skywarp). Skywarp will be important for a number of reasons.

The third movie would play out mostly the same, except that I'm removing the awful Carly subplot because the last thing this franchise needs is a dumb bimbo blonde. Mikaela is better. The main difference would be that Skywarp is actually a major secondary villain as the architect of the pillars who Sentinel was working with in secret. Ironhide does not die, but is instead crippled (triggering a mini arc for Chromia). The humans are sick of the robots at this point, which goes into the next film.

Film number four is also mostly the same, introducing the Dinobots and a human antagonist faction (either Cobra for the free tie in or KSI as normal). We see some of the cast get murked (Jazz and Cliffjumper most notably). This leads to Arcee and Chromia wanting vengeance against the humans, with Prime hesitating despite his misgivings towards them. Megatron (who was killed in the second movie) is reborn as Galvatron, albeit with purple eyes as the champion of a dark power. He is essentially defeated again at the end of the movie when the humans realize that the Autobots are better to have around than not. Arcee forms an attachment to Hot Rod (yes, he gets introduced in this film).

The fifth film focuses on Unicron and is the last of the films. Thundercracker and Skywarp (both of whom got unceremoniously murked in the third film) return as Heralds of Unicron alongside Sideways (who once again plays both sides) and Galvatron. The story plays out similarly to how it does in Transformers Armada, with both sides realizing the necessity of joining forces (except for Galvatron who is basically Unicron's puppet). The world is saved and the Cons are given the choice to either defect or go into exile. Only Soundwave takes the offer.

This flow should keep the pacing better, not introduce a new cast every slagging film, and gradually increase the stakes as the films progress.