The UAF tenure had a rather odd tendency to retcon plot points from the original series for no apparent reason and often in ways that didn't make much sense, and even retconned events within the UAF tenure itself in ways that didn't make much sense. Here's a list of the ones I can recall.
Retcons between TOS and UAF continuity
- Plumbers were changed from an Earth-based paranormal investigation/protection force to an intergalactic police force, displacing the Galactic Enforcers who were apparently an alien Justice League. In TOS, they were largely retired with a skeleton crew remaining, while in UAF they were fully staffed and active across the galaxy.
- Azmuth went from cynical, pessimistic, sarcastic, and the smartest guy in the universe to "First Thinker," the insufferably arrogant, self-righteous ruler of Galvan Prime who rewrote the laws whenever it suited him.
- Vilgax was a cruel, terrible megalomaniac who had long feuded with the plumbers and would wipe out an entire world when it suited him. In UAF he was reduced to stealing super powers from aliens to stand a chance against Ben, was famous for conquering merely ten worlds, and was the beloved benevolent ruler of Vilgaxia.
- The Galactic Enforcers were apparently an alien equivalent to the Justice League. Unfortunately, even though they tried to impose their "Galactic Code of Conduct," they were ignored more often then not by anyone with a firearm in a more or less lawless galaxy. In UAF they were reduced to a one-note joke with absolutely no relevance and never appeared again, while the plumbers became a largely successful galactic police force.
- Magic was made into Mana. This was far less jarring because it was an almost entirely cosmetic change.
- Kevin was changed from a mutant to an alien hybrid, and this was implied to be the case for Michael and Cooper. This isn't particularly jarring because Kevin's species was never stated in TOS, only in writer interviews, and alien hybrids were clearly shown to exist in TOS.
- When Eon appeared in UAF, Ben clearly stated he encountered him before, meaning that RAT is canonical. However, Eon was changed from a Chronian to an Evil!Ben from an alternate universe. The Hands of Armageddon were changed from a key to the Chronian's prison to a doorway between parallel universes; the Hands had previously been destroyed and then reappeared intact with no explanation despite it later being explained that when the Hands were destroyed a second time it destroyed the Hands in all parallel universes.
Retcons within UAF continuity
- The Omnitrix was originally stated in AF to contain a DNA database, then a later AF episode contradicted this and stated the DNA database was located on Primus.
- The queen in Alien Swarm was later stated to be a decoy and Elena was the real queen the whole time. This retcon doesn't make a lot of sense and only makes Elena look schizophrenic. Why did Elena come to Ben for help to stop the decoy queen if she was controlling the chips the whole time? Why did Elena stop trying to take over the world after the decoy queen was killed and decide to try using the chips to help mankind?
Are there any retcons I'm missing?