It depends where you live. For example in France, the price equivalement of the 540R is the Marantz 5400 OSE.
It seems that they are both quite good in hifi which is not very common for a HC receiver. But they sound very different depending on which speakers you have, so it would be best to listen to both of them on your speakers before making a decision.
Here in the UK the equivalent to the SR6400 is the 5400 OSE and that can be had for £378 online (MRSP of £550) and the 540R is available for £250 (same as from the off). A not insignificant difference. Generally though the 4400 is considered the equivalent to the 540R in price and possibly performance terms.
Agree with Falp about the Marantz 4400 LFE crossover setting. I would like to have used one at 80Hz. I'm not entirely convinced 100Hz is ideal for a sub.
I would take the 5400OSE over the 540R, but I dont know if the 6400 is as good as the OSE. The Marantz have more features but the 540R is nice and simple with good sound.