I wouldn't really say that it's a flaw of Metacritic in general.
It's either a flaw of:
Reviewers rating the game too high
The game being insignificant, so there aren't a lot of reviews and diversity
Or Metacritic didn't spend enough time hunting for reviews (but again, that's due to the obscurity of the game)
I think that it's a very good indicator of what the general reception for a work is.