Prince of Persia, from 6th to 7th gen.
Megaman X, true greatness during the 16 bit era, then X4 on PS also great, X5 decent, X6 awful. Then, next gen X7... wtf...
Street Fighter 4 on PS3/360 to Street Fighter 5 on PS4.
Also agree with Mass Effect.
Deus Ex HR to Deus Ex MD also comes to mind.