The characters missing are the Predicons/Destolonger, Spychangers, Skids/Indy Heat, Towel Line/Wrecker Hook, the Decepticons/Combatrons (their combined form Ruination/Baldigas), & Fortress/Brave Maximus.
Transformations now have become so predictable and G1 based. This era and the early movie era were the most creative with lots of asymmetry and puzzling body part conversions, although the mysterious transformations were kind of a double edged sword for kids. Armada/マイクロン伝説 was also pretty unique in its style but they simplified the transformations and blocked up the toys. The post Animated kids-aimed shows have kind of painted itself into a corner with the toys' slavish adherence the stylised US animation style, it leaves little to the child's imagination to fill in the gaps. Slightly challenging, interesting, yet simple transformations for toys, along with more anthropomorphised fictional counterparts is the best approach to keep kids interested IMHO, but they are all stuck in the iPads now so whatever.