MKA was never a good story-telling game to begin with - gameplay took precedence over the story, which was one big mess obviously and as far as Mavado is concerned, MKA improved his moveset greatly by adding more special moves involving his signature grappling hooks and power-up ability. When it comes to his position in the clan, Mavado was never stated to be the leader of the Red Dragon, Daegon was its only founder and leader, therefore I do not think his position in the clan has changed from MKDA to MKA. It was a mistake however, to keep the hookswords with Mavado WHILE Kabal had them too. Li Mei used to have Mileena's sai in MKDA but as soon as Mileena returned in MKD, Li Mei's weapon was changed to a sword. This sadly did not occur in Mavado's case and it largely contributed to the perception of him being a ripoff of Kabal.