It's tough because it's a bit of an apples-to-oranges comparison, given the two completely different ride systems.
I'd say Mummy is the better attraction, but only because I enjoy the story and theming and humor of the Mummy more than I enjoy the earnest vehicular violence of Transformers (plus, I tend to see Transformers as a well-done, but still inferior, retread of Spider-Man). I like them both though, and would never miss either one.