Great game, loved it. Only problem is it got a bit easy. I beat a couple levels in as low as 18 seconds. =/
The best thing to do is to quickly gain control over as many cells as possible at the start of each level.
Inklink is better than this, the only advantages this one has is that if someone else gets it first you still have a chance, and there aren't as many *** holes in this game.
A great strategy is to use around 5 defenders to distract their samurais, and then have the rest be ninjas and go past their front lines, and attack their long range men. Then just stay far away from their front lines and you'll win.