It's pretty bad, but that's mostly wrapped up in being one of the most crass toy commercials in history. The first 25 minutes is just an excuse to murder off the existing toys so the new toys can take over, and kinda doesn't have a lot to do with the main plot of Unicron. (Or, conversely, the Unicron plot takes over the existing autobot/decepticon plot)
Then the movie faffs about for like 30 minutes to introduce MORE toys and characters that aren't even important to that plot.
When we finally get back that plot,it's resolved in like ten minutes due to MacGuffin.
The dialog isn't bad and is well voice acted, the animation and action is great, and the music is fantastic.
But the actual story is mostly garbo. Like the first 25 minutes, sans Unicron, makes kind of a metal capstone to the cartoon, despite being tonally inconsistent to the show, but it's an overly long way of clearing out the cast and getting the Matrix in position to eventually wind up in Hot Rod's hands.
Even Hot Rod's hero's journey is half-assed. We see glimmers of greatness (Like him apparently being a skilled enough medic to repair Kup, or when he negotiates with the Junkions, remembering the universal greeting) but it's very light because there's 50,000 other things going on because we need to show off Wreck-Gar and Wheelie and the Sharkticons, and also the Dinobots are still on shelves so let's give them an extended sequence of literally wandering around lost.
Make no mistake, I find that movie near and dear to my heart, but even for the time it has a terrible, terrible plot.
But also who cares, the movie is a 90 minute hair metal fever dream. It gets by without a good story.