Remember that the Yamaha was originally £800 and the Onkyo £400 - when you bear that in mind, it's no surprise the Yamaha sounds more controlled and refined. You'll hear more detail and scale from your Blu-rays - and if you want to spin the odd CD, it'll sound better, too.
But the Onkyo remains an incredibly dynamic, exciting receiver for the money - it's a victim of Yamaha's aggressive pricing and the more sophisticated approach of some other rivals rather than any inherent shortcoming.