The episode 4 was only added on screen in a re-release from 1981, after it was decided that Empire was going to be Episode 5. While Lucas may have planned to have 3, 6, 9, or 12 films all along, the stories themselves were always being made up as he went along. It's the same with any series. You do one storyline movie at a time. If you don't believe me, check out some of the reviews for the very first Empire Strikes Back screenplay from Leigh Bracket: virtually nothing is the same as what we saw on screen.
This new Transformers franchise is no different. They're making it up as they go along. There is no grand plan or cosmic design.