I'm willing to bet the Arcam will sound much better. The AV9 was a beast of a Pre-Amp and still is except it lacks the Sound EQ, which does little to nothing on the 3900 other than setup sound levels, crossovers and speaker distances. The Crossovers are not even accurate. I had the 3900 for a month and returned it. It's a good AVR, but no way will it compare to an AV9 with a good 5 channel Amp.
The only other thing lacking is HD audio codecs in the Arcam, but the Arcams ability to deliver depth and imaging will far outshine the HD audio of the Yamaha. At least that's my opinion when comparing the 3900 to the AVR350..