I had the same issue, but I found a solution that worked for me with the third person C++ template. In the constructor for the default GameModeBase class, I removed the following lines:
static ConstructorHelpers::FClassFinder<APawn> PlayerPawnBPClass(TEXT("/Game/ThirdPerson/Blueprints/BP_ThirdPersonCharacter"));
if (PlayerPawnBPClass.Class != NULL)
{
DefaultPawnClass = PlayerPawnBPClass.Class;
}
I think the issue might be that this code gets executed before the motion matching-related plugins are loaded in, resulting in a blueprint that has references to non-existing classes.