Re: Michael Bay out of the way!
The story in ROTF was definitely worse that the first in terms of narrative & pacing. There was also an over saturation of comedy (usually hit or miss).
The first films script wasn't gold but it was structured in a much better way than the script for ROTF was.
Not only that but the already simplistic dialogue for the humans was lowered a notch as well. I mean in one sentence Sam uses the word "head" almost consecutively to explain that Megatron was trying to get the ancient Cybertronian language from his brain.
Thats just one example out of many. The plot itself wasn't bad but the manner in which it was structured largely caused ROTF to drag severely throughout parts. I mean during my first viewing I was lethargic by the time Jet Prime came onto the screen.