Comparison by:
Abilities - Magic Guard Clefable is one of the best abilities out there, as it prevents indirect damages especially from Reborn well known field effects, unaware gets less use as AI rarely uses boosting moves. While with Gothitelle, it has competitive, which is situational in game, other two abilities also are less useful in game wise(Frisk can scout wild held items but that's it), in this aspect, Clefable gains the upperhand
Movepool - Clefable has wider movepools with access to flamethrower and psychic to check its greatest threats, poison and steel whereas Gothitelle cannot check dark types
Type advantages and disadvantages - Clefable as pure fairy type has two weaknesses, three resistances and one immunity which we will be battling one of the gym leaders from, while Gothitelle pure psychic has two weaknesses, no immunity and two resistances, so Clefable also stands out in this aspect
Stat - They are even in term of tanking, and base special attack is almost the same.
Overall, the replacement is pretty justifiable.