I've traveled this route before. There is a bus linking Onomichi and Innoshima and another bus linking Innoshima and Imabari for 2,200 JPY one-way which will be your best bet (though the transfer is a bit of a pain, you stop at a service area which has facilities). You could also take a direct bus to Fukuyama from Imabari, then travel to Onomichi on the Shinkansen, though this will obviously cost more.

Otherwise you could rent a car, but for a <2 hour trip it's probably not worth it.