Do a lot of pivot grabbing. For some reason, Ike's has tons of ghost reach and long-lasting grab boxes.
If you're both at low percents, you can test a dthrow->aether and see how they VI. If they know how to get out of it, do dthrow->aerial the next time. Greninja has just as much landing lag on aerials as we do, so he's going to try to stay on the ground and in the air only when we are, too.
Always keep this in mind: 80% for partially charged usmash, ~95-100 for uncharged usmash, 110 for utilt for easy kills. Go after both Greninja and Falco offstage and follow where they're going. Fair wall is the easiest to get going.
At mid %s, nair->fair/uair and just chase them. Nair just combos into almost anything you want most of the time.
Currently 92-4, 1 loss with Mega Man, so I'm not spouting complete BS.