I can't comment on TCGs outside of MtG, but this is not considered sufficient shuffling in Magic tournaments (you may pile shuffle to count the cards in your deck, but it is not enough on its own). I would be surprised to find out that it's not also considered cheating in other games as well, since it is extremely easy to manipulate the location of cards while seeming to randomize your deck using this method, if you know what you're doing.

That said, in casual board game play, I don't see the issue with doing it.