I have been contemplating the pairing of Ninjask and Shedinja, and I have an idea for a neat set up using the pair of Ninja Pokemon.
Ninjask Baton Pass Lead w/ Focus Sash
Substitute/ Double Team
Shedinja PP Stall w/ Safety Goggles
Ninjask is used here as you would see it almost everywhere else. You start your turn by either using Protect, if you feel some rocks coming, Substitute, if you feel a status coming, or U-Turn if you think the adversary is an Infiltrator. Consider U-Turn your mulligan/ scouting move. Ok. You stay in and get your Speed Boosts for as long as fragile Ninjask can hold out. I know Smogon forbades Double Team, but if you've played on Battle Spot, you know they don't share Smogon's rules on this (I'm looking at you, Minimize Blissey). So, Double Team is an excellent option in lieu of Substitute, but either are good options. Now, you've got +2-4 Speed Boosts; as long as the field is clear of Spikes, T.Spikes, or S. Rock, your Shedinja is good to go. If not, keep a Rapid Spinner, go to that, and try again later. This strategy works best after some threats have been taken out anyways, but if you can get a Ninjask with Defog, this may also be an option for you.
Shedinja comes in, with either a Sub or some Double Team boosts. Safety Goggles is going to protect you from Sandstorm or Hail damage; a Sub will protect you from status conditions. Your opponent may take this turn to Switch In a Super Effective Counter. You have options. You can set your Grudge up, which will make your opponent think twice about having it's PP drained next turn. Or, you can fade out using Phantom Force and come back in next turn. If they brought in a Normal type, that's still fine. This Shedinja doesn't try to beat you by being a better attacker; it tries to drain your opponent's ability to effectively fight your team. Spite is the go to move for this. If your opponent tried to attack you while you were phazed due to Phantom Force, come back in and Spite the move they used last. That's 5 PP drained from the move, easily. Do it again, and your opponent may not be able to attack your Shedinja as effectively. If you feel that your opponent is packing a super effective move, Endure the hit and Spite/ Grudge next turn. Thats another 5 PP drained. But beware; at the first chance you don't have a Sub and you've noticed your opponent packing Toxic/ Will o Wisp, get Shedinja out of there and try again later. In Singles, Shedinja has no way of protecting against status, unless you've had a chance to set up Safeguard, possibly with the same Pokemon who uses Rapid Spin?
This is fairly gimmicky. I came up with the idea when I was developing a Bug Team. Let me know if you think this might be effective. I'm going to nab a Nincada and try it out for myself, but... I've always wanted a Pokemon that could take advantage of moves like Spite and abilities like Pressure because if you can't use your Pokemon's moves, then you can't beat your opponent. It's a win condition people often forget about until it's too late.