It's pretty amazing, looking back. This movie was an incredibly cynical marketing ploy turned out to be a Serious Movie for Kids.
I loved the Transformers as a kid, and this movie was eye-opening. It showed that stuff I liked could be serious, could deal with major, emotional themes. It was probably the first thing I saw that didn't treat kids like delicate snowflakes: entire planets are destroyed, well-known characters are clearly killed on screen. It felt like the stakes were so much higher, and I loved it, even if I didn't quite have the emotional equipment to process it.
As a kid whose susceptibility to clinical levels of anxiety was starting to manifest, Unicron was terrifying. I remember more than a few sleepless nights (for me and my mom both) because I would have vivid images of Unicron showing up and eating the Earth. Seriously, if you were 4 years old living under the still-present threat of nuclear holocaust, giant and unstoppable forces based on technological sophistication were the new boogeymen.