Kinda needs a note of Cresselia which seems to be in a ton of war stories and RMTs, same for Blissey really. The latter seems to be using Sing and Thunderbolt and all kinds of whacko stuff. I suspect Tyranitar may not be used as much simply because it is an absolute pain to breed for.
Ninjask is practically nonexistant, probably due to the new and improved Taunt. However, it should catch on when people let their guard down and don't use Taunt or a good pseudohazer.
I don't get this, really. Taunt is not a Ninjask counter because it doesn't go through Substitute and Ninjask will always be able to get in :something: before the Taunt as its so insanely fast. The main reason I'd say Ninjask isn't used much is because Skarmory is guaranteed to blow it out now and you can't simply pass to Magneton anymore and say "no way out now kid". Or simply because people aren't training up a Ninjask first - they're trying out old favourites that improved a bunch, or new hyped Pokemon like Garchomp, Rhyperior and Electrivire.